Design of a marker-based human motion tracking system

In this paper a complete design of a high speed optical motion analyzer system has been described. The main core of the image processing unit has been implemented by the differential algorithm procedure. Some intelligent and conservative procedures that facilitate the search algorithm have also been proposed and implemented for the processing of human motions. Moreover, an optimized modified direct linear transformation (MDLT) method has been used to reconstruct 3D markers positions which are used for deriving kinematic characteristics of the motion. Consequently, a set of complete tests using some simple mechanical devices were conducted to verify the system outputs. Considering the system verification for human motion analysis, we used the system for gait analysis and the results including joint angles showed good compatibility with other investigations. Furthermore, a sport application example of the system has been quantitatively presented and discussed for Iranian National Karate-kas. The low computational cost, the high precision in detecting and reconstructing marker position with 2.39 mm error, and the capability of capturing from any number of cameras to increase the domain of operation of the subject, has made the proposed method a reliable approach for real-time human motion analysis. No special environment limitation, portability, low cost hardware and built in units for simulations and kinematic analysis are the other significant specifications of this system.     

Influence of the correlation modeling period on the prediction accuracy of infrared marker-based dynamic tumor tracking using a gimbaled X-ray head

PurposeTo assess the utility of 10 s and 20 s modeling periods, rather than the 40 s currently used, in the clinical construction of practical correlation models (CMs) in dynamic tumor tracking irradiation using the Vero4DRT.MethodsThe CMs with five independent parameters (CM parameters) were analyzed retrospectively for 10 consecutive lung cancer patients. CM remodeling was performed two or three times per treatment session. Three different CMs trained over modeling periods of 10, 20, and 40 s were built from a single, original CM log file. The predicted target positions were calculated from the CM parameters and the vertical displacement of infrared markers on the abdomen (P_IR) during the modeling. We assessed how the CM parameters obtained over modeling periods of T s (T = 10, 20, and 40 s) were robust to changes in respiratory patterns after several minutes. The mimic-predicted target positions after several minutes were computed based on the previous CM parameters and P_IR during the next modeling. The 95th percentiles of the differences between mimic-predicted and detected target positions over 40 s (E95_robust,T: T = 10, 20, and 40 s) were then calculated.ResultsStrong correlations greater than 0.92 were observed between the E95_robust,20 and E95_robust,40 values. Meanwhile, irregular respiratory patterns with inconsistent amplitudes of motion created differences between the E95_robust,10 and E95_robust,40 values of ≥10 mm.ConclusionsThe accuracies of CMs derived using 20 s were almost identical to those obtained over 40 s, and superior to those obtained over 10 s.     

Static and dynamic errors in particle tracking microrheology

Particle tracking techniques are often used to assess the local mechanical properties of cells and biological fluids. The extracted trajectories are exploited to compute the mean-squared displacement that characterizes the dynamics of the probe particles. Limited spatial resolution and statistical uncertainty are the limiting factors that alter the accuracy of the mean-squared displacement estimation. We precisely quantified the effect of localization errors in the determination of the mean-squared displacement by separating the sources of these errors into two separate contributions. A "static error" arises in the position measurements of immobilized particles. A "dynamic error" comes from the particle motion during the finite exposure time that is required for visualization. We calculated the propagation of these errors on the mean-squared displacement. We examined the impact of our error analysis on theoretical model fluids used in biorheology. These theoretical predictions were verified for purely viscous fluids using simulations and a multiple-particle tracking technique performed with video microscopy. We showed that the static contribution can be confidently corrected in dynamics studies by using static experiments performed at a similar noise-to-signal ratio. This groundwork allowed us to achieve higher resolution in the mean-squared displacement, and thus to increase the accuracy of microrheology studies.     

Simulated four-dimensional CT for markerless tumor tracking using a deep learning network with multi-task learning

IntroductionOur markerless tumor tracking algorithm requires 4DCT data to train models. 4DCT cannot be used for markerless tracking for respiratory-gated treatment due to inaccuracies and a high radiation dose. We developed a deep neural network (DNN) to generate 4DCT from 3DCT data.MethodsWe used 2420 thoracic 4DCT datasets from 436 patients to train a DNN, designed to export 9 deformation vector fields (each field representing one-ninth of the respiratory cycle) from each CT dataset based on a 3D convolutional autoencoder with shortcut connections using deformable image registration. Then 3DCT data at exhale were transformed using the predicted deformation vector fields to obtain simulated 4DCT data. We compared markerless tracking accuracy between original and simulated 4DCT datasets for 20 patients. Our tracking algorithm used a machine learning approach with patient-specific model parameters. For the training stage, a pair of digitally reconstructed radiography images was generated using 4DCT for each patient. For the prediction stage, the tracking algorithm calculated tumor position using incoming fluoroscopic image data.ResultsDiaphragmatic displacement averaged over 40 cases for the original 4DCT were slightly higher (<1.3 mm) than those for the simulated 4DCT. Tracking positional errors (95th percentile of the absolute value of displacement, “simulated 4DCT” minus “original 4DCT”) averaged over the 20 cases were 0.56 mm, 0.65 mm, and 0.96 mm in the X, Y and Z directions, respectively.ConclusionsWe developed a DNN to generate simulated 4DCT data that are useful for markerless tumor tracking when original 4DCT is not available. Using this DNN would accelerate markerless tumor tracking and increase treatment accuracy in thoracoabdominal treatment.     

Development of a markerless gene knock-out system for Mannheimia succiniciproducens using a temperature-sensitive plasmid

A temperature-sensitive derivative of the Mannheimia varigena plasmid pMVSCS1 was constructed by hydroxylamine treatment for use in the development of a markerless gene knock-out system for Mannheimia succiniciproducens. The temperature-sensitive plasmid pMVSCS1-ts was stably maintained at 30 degrees C, but failed to replicate at 42 degrees C. DNA sequencing of the replication origin revealed a single base substitution as being responsible for its temperature sensitivity. The region of replication origin was amplified by PCR to construct an Escherichia coli-M. succiniciproducens shuttle vector pME19-ts to further examine the thermosensitivity. To make markerless mutants of M. succiniciproducens, the Cre-lox system with the variant lox66 and lox71 sites was used to prevent the instability caused by multiple loxP sites in the genome. The transient cre expression was carried out using the temperature-sensitive plasmid pCRX5, which was consequently cured after the verification of the markerless mutant by growing cells at 42 degrees C. For the demonstration of the markerless deletion of multiple genes using this method, the ldhA gene and the oadGAB operon of M. succiniciproducens encoding lactate dehydrogenase and oxaloacetate decarboxylase, respectively, were successfully deleted sequentially. This markerless deletion method should be useful for further metabolic engineering of M. succiniciproducens, which is a promising industrial bacterium for succinic acid production from renewable resources.     

Three-dimensional comparison of static and dynamic scapular motion tracking techniques

The shoulder is complex and comprised of many moving parts. Accurately measuring shoulder rhythm is difficult. To classify shoulder rhythm and identify pathological movement, static measures have been the preferred method. However, dynamic measures are also used and can be less burdensome to obtain. The purpose of this paper was to determine how closely dynamic measures represent static measures using the same acromion marker cluster scapular tracking technique. Five shoulder angles were assessed for 24 participants using dynamic and static tracking techniques during humeral elevation in three planes (frontal, scapular, sagittal). ANOVAs were used to identify where significant differences existed for the factors of plane, elevation angle, and tracking technique (static, dynamic raising, dynamic lowering). All factors were significantly different for all shoulder angles (p < 0.001), except for elevation plane in scapulothoracic protraction/retraction (p = 0.955). Tracking techniques were influential (p < 0.001), but the grouped mean differences fell below a clinically relevant 5° benchmark. There was large variation in mean differences of the techniques across individuals. While population averages are similar, individual static and dynamic shoulder assessments may be different. Caution should be taken when dynamic shoulder assessments are performed on individuals, as they may not reflect those obtained in static scapular motion tracking.     

Accuracy and repeatability of joint angles measured using a single camera markerless motion capture system

Markerless motion capture systems have developed in an effort to evaluate human movement in a natural setting. However, the accuracy and reliability of these systems remain understudied. Therefore, the goals of this study were to quantify the accuracy and repeatability of joint angles using a single camera markerless motion capture system and to compare the markerless system performance with that of a marker-based system. A jig was placed in multiple static postures with marker trajectories collected using a ten camera motion analysis system. Depth and color image data were simultaneously collected from a single Microsoft Kinect camera, which was subsequently used to calculate virtual marker trajectories. A digital inclinometer provided a measure of ground-truth for sagittal and frontal plane joint angles. Joint angles were calculated with marker data from both motion capture systems using successive body-fixed rotations. The sagittal and frontal plane joint angles calculated from the marker-based and markerless system agreed with inclinometer measurements by <0.5°. The systems agreed with each other by <0.5° for sagittal and frontal plane joint angles and <2° for transverse plane rotation. Both systems showed a coefficient of reliability <0.5° for all angles. These results illustrate the feasibility of a single camera markerless motion capture system to accurately measure lower extremity kinematics and provide a first step in using this technology to discern clinically relevant differences in the joint kinematics of patient populations.     

Kinematic parameters of throwing performance in patients with schizophrenia using a markerless motion capture system

Abstract

Motor dysfunction is consistently reported but understudied in schizophrenia. It has been hypothesized that this abnormality may reflect a neuro-developmental disorder underlying this illness. The main goal of this study was to analyze movement patterns used by participants with schizophrenia and healthy controls during overarm throwing performance, using a markerless motion capture system. Thirteen schizophrenia patients and 16 healthy control patients performed the overarm throwing task in a markerless motion capture system. Participants were also examined for the presence of motor neurological soft signs (mNSS) using the Brief Motor Scale. Schizophrenia patients demonstrated a less developed movement pattern with low individualization of components compared to healthy controls. The schizophrenia group also displayed a higher incidence of mNSS. The presence of a less mature movement pattern can be an indicator of neuro-immaturity and a marker for atypical neurological development in schizophrenia. Our findings support the understanding of motor dysfunction as an intrinsic part of the disorder of schizophrenia.     

Marker removal system for Thermoanaerobacterium saccharolyticum and development of a markerless ethanologen

Marker removal strategies were developed for Thermoanaerobacterium saccharolyticum to select against the pyrF gene and the pta and ack genes. The pta- and ack-based haloacetate selective strategy was subsequently used to create strain M0355, a markerless Δldh Δpta Δack strain that produces ethanol at a high yield.     

Static and dynamic imaging of alveoli using optical coherence tomography needle probes

Imaging of alveoli in situ has for the most part been infeasible due to the high resolution required to discern individual alveoli and limited access to alveoli beneath the lung surface. In this study, we present a novel technique to image alveoli using optical coherence tomography (OCT). We propose the use of OCT needle probes, where the distal imaging probe has been miniaturized and encased within a hypodermic needle (as small as 30-gauge, outer diameter 310 μm), allowing insertion deep within the lung tissue with minimal tissue distortion. Such probes enable imaging at a resolution of ～12 μm within a three-dimensional cylindrical field of view with diameter ～1.5 mm centered on the needle tip. The imaging technique is demonstrated on excised lungs from three different species: adult rats, fetal sheep, and adult pigs. OCT needle probes were used to image alveoli, small bronchioles, and blood vessels, and results were matched to histological sections. We also present the first dynamic OCT images acquired with an OCT needle probe, allowing tracking of individual alveoli during simulated cyclical lung inflation and deflation.     

Static and dynamic properties of gravity-sensitive receptors in the cat vestibular system

Summary The spike activity of eighth cranial nerve units tonically responsive to head position was recorded in cats anesthetized with pentobarbital sodium, and related with linear accelerations induced by gravity during maintained positions and during dynamic trajectories achieved through rolling around a rostro-caudal axis.The steady-state discharge of 80% of the cells had relatively small coefficients of variation, narrow histograms and periodic autocorrelograms. That of most remaining cells had large coefficients variation, nearly exponential histograms and flat or weakly periodic autocorrelograms.The static relation between head position and discharge showed that each cell had directional sensitivity, i.e. a characteristic change associated with each movement sense. Sixty-six percent of the cells had side-up increases in interval mean and standard deviation, with translation of the histogram to the right and reduction in the average autocorrelogram value: 34% had the opposite relations. Many cells showed multivaluedness, i.e. the interval mean (and other statistics) from different stations at any given position covered a range greater than that at each station. Multivaluedness varied from cell to cell.In the dynamic experiments the discharge was recorded during a continuous motion that involved a single sine wave or a mixture of sinusoids at frequencies up to 0.1 Hz. The spike trains exhibited a continuous mapping of the time varying tilt angle into the instantaneous rate with little or no evidence of multivaluedness. In addition to a tonic part, responses showed a phasic component with the characteristics of a unidirectional rate sensitivity that determined a phase-lead of the response with respect to the stimulus. The relative proportions of tonic and phasic components varied from cell to cell.Based upon anatomical and mechanical considerations (see Appendix) and upon the present results it is suggested that deformations of the trampoline-like membrane occur in a distributed manner. Multivaluedness may be due to forces which, like stiction, prevent complete relaxation of the membrane under static but not under dynamic conditions. The phasic response, whose origin is obscure, argues in favor of the otolithic receptors having a dynamic function, in addition to their role in detecting head positions with respect to gravity.     

Comparison of headspace techniques for sampling volatile natural products in a dynamic system

Commonly used dynamic sorption techniques for collecting biologically active volatile compounds have been compared. Solid phase microextraction (SPME) using two types of fibers (polydimethylsiloxane, PDMS, 100 microm, and carbowax/divinylbenzene, CW/DVB, 65 microm) was compared to purge and trap methods (Porapak Q, Tenax TA and charcoal) and a technique based on absorption in methanol in a cooling bath. Sampling was done in a stream of purified air (20 ml/min) in a closed and temperature-regulated (27 degrees C) glass tube, passing over a capillary tube containing a hexane solution of tridecane, heptadecane, 1-octen-3-ol, 1-hexadecanol, ethyl tetradecanoate, alpha-pinene, linalool, terpinen-4-ol, cis-verbenol, verbenone, beta-caryophyllene, E,E-farnesol, and geranylgeraniol. With all of the methods, the sampling was performed for a period of 30 min before extraction and analysis was done on a GC-FID system. In general, SPME gave a higher response for all compounds except for alpha-pinene, which was only extracted by the CW/DVB fiber. Purge and trap methods and methanol absorption gave the same response for all substances extracted. None of the methods extracted hexadecanol and geranylgeraniol under the conditions used. However, the SPME equipped with the PDMS coating extracted heptadecane, E,E-farnesol and ethyl tetradecanoate. Our results show that SPME, when selecting the fibers to fit the polarity and volatility of the compounds, is an outstanding extraction method compared to purge and trap and methanol absorption, especially for a qualitative analysis. The best conditions for storing fibers exposed to compounds of high volatility were at low temperatures (6 degrees C) in sealed vials, while the worst way was to leave the exposed fiber unprotected at room temperature (22 degrees C). The dynamic sampling system was effectively tested on a fruiting body of a polypore fungus (Ganoderma applanatum) emitting 1-octen-3-ol, and again SPME showed to be the most sensitive technique.     

Static and dynamic operating characteristics of a pericardial balloon.

Previously, we developed a balloon transducer to measure the constraint of the pericardium (i.e., pericardial pressure) on the surface of the heart. It was validated physiologically in that it was shown to measure a pressure equal to the difference between the left ventricular end-diastolic pressure measured before and after pericardiectomy at the same left ventricular volume. To define its static operating characteristics, we loaded the balloon nonuniformly with weights that covered fractions of the balloon surface and found that the balloon accurately recorded the average stress if the stress was applied over at least 23% of its surface. To test its performance when curved, we placed it in large and small cylinders (minimum diameter 31 mm) and found that the balloon accurately recorded the stress. To define its dynamic operating characteristics, we applied sinusoidal stresses and found that its frequency response was limited only by that of the connecting catheter. When better dynamic response is required, we introduce a micromanometer-tipped catheter to obtain a unity-gain frequency response that is flat to 200 Hz.     

Development of a novel genetic system to create markerless deletion mutants of Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is a species of unique obligate predatory bacteria that utilize gram-negative bacteria as prey. Their life cycle alternates between a motile extracellular phase and a growth phase within the prey cell periplasm. The mechanism of prey cell invasion and the genetic networks and regulation during the life cycle have not been elucidated. The obligate predatory nature of the B. bacteriovorus life cycle suggests the use of this bacterium in potential applications involving pathogen control but adds complexity to the development of practical genetic systems that can be used to determine gene function. This work reports the development of a genetic technique for allelic exchange or gene inactivation by construction of in-frame markerless deletion mutants including the use of a counterselectable marker in B. bacteriovorus. A suicide plasmid carrying the sacB gene for counterselection was used to inactivate the strB gene in B. bacteriovorus HD100 by an in-frame deletion. Despite the inactivation of the strB gene, B. bacteriovorus was found to retain resistance to high concentrations of streptomycin. The stability of a plasmid for use in complementation experiments was also investigated, and it was determined that pMMB206 replicates autonomously in B. bacteriovorus. Development of this practical genetic system now facilitates the study of B. bacteriovorus at the molecular level and will aid in understanding the regulatory networks and gene function in this fascinating predatory bacterium.     

Estimation and validation of spatio-temporal parameters for sprint running using a radio-based tracking system

Spatio-temporal parameters like step length, step frequency and ground contact time are directly related to sprinting performance. There is still a lack of knowledge, however, on how these parameters interact.Recently, various algorithms for the automatic detection of step parameters during sprint running have been presented which have been based on data from motion capture systems, video cameras, opto-electronic systems or Inertial measurement units. However, all of these methods suffer from at least one of the following shortcomings: they are (a) not applicable for more than one sprinter simultaneously, (b) only capable of capturing a small volume or (c) do not provide accurate spatial parameters. To circumvent these issues, the radio-based local position measurement system RedFIR could be used to obtain spatio-temporal information during sprinting based on lightweight transmitters attached to the athletes. To assess and optimize the accuracy of these parameters 19 100 m sprints of twelve young elite athletes (age: 16.5 ± 2.3 years) were recorded by a radio-based tracking system and a opto-electronic reference instrument. Optimal filter parameters for the step detection algorithm were obtained based on RMSE differences between estimates and reference values on an unseen test set. Attaching a transmitter above the ankle showed the best results.Bland-Altman analysis yielded 95% limits of agreement of [−14.65 cm, 15.05 cm] for step length [−0.016 s, 0.016 s] for step time and [−0.020 s, 0.028 s] for ground contact time, respectively. RMS errors smaller than 2% for step length and step time show the applicability of radio-based tracking systems to provide spatio-temporal parameters. This creates new opportunities for performance analysis that can be applied for any running discipline taking place within a stadium. Since analysis for multiple athletes is available in real-time this allows immediate feedback to coaches, athletes and media.     

Direct comparison of kinematic data collected using an electromagnetic tracking system versus a digital optical system

The purpose of this study was to quantify the dynamic accuracy of kinematics measured by a digital optical motion analysis system in a gait analysis laboratory (capture volume approximately 20m(3)) compared to a standard range direct-current electromagnetic (EM) tracking device (capture volume approximately 1m(3)). This is a subset of a larger effort to establish an appropriate marker set for the optical system to quantify upperlimb kinematics simultaneously with gait, in comparison to previous studies of isolated upperlimb movements that have employed EM tracking devices. Rigid clusters of spherical reflective markers and EM sensors were attached to a mechanical articulator that mimicked three-dimensional joint rotations, similar to the elbow. As the articulator was moved through known ranges of motion (i.e. gold standard), kinematic data were collected simultaneously using both tracking systems. Both systems were tended to underestimate the range of motion; however, the application of post hoc smoothing and least-squares correction algorithms reduced these effects. When smoothing and correction algorithms were used, the magnitude of the mean difference between the gold standard and either the EM or optical system did not exceed 2 degrees for any of the compound motions performed. This level of agreement suggests that the measurements obtained from either system are clinically comparable, provided appropriate smoothing and correction algorithms are employed.     

An efficient system for markerless gene replacement applicable in a wide variety of enterobacterial species

We describe an improved allelic-exchange method for generating unmarked mutations and chromosomal DNA alterations in enterobacterial species. Initially developed for use in Salmonella enterica, we have refined the method in terms of time, simplicity, and efficiency. We have extended its use into related bacterial species that are more recalcitrant to genetic manipulations, including enterohemorrhagic and enteropathogenic Escherichia coli and Vibrio parahaemolyticus. Data from over 50 experiments are presented including gene inactivations, site-directed mutagenesis, and promoter exchanges. In each case, desired mutations were identified by polymerase chain reaction screening typically from as few as 10-20 colonies up to a maximum of 300 colonies. The method does not require antibiotic nor nutritional markers in target genes and works efficiently in wild-type strains, obviating the need for specialized hosts or genetic systems. The use is simple, requiring basic laboratory materials, and represents an alternative to existing methods for gene manipulation in the Enterobacteriaceae.