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44 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>
OpenArm: Volumetric & Time Series Models of Muscle Deformation
- We invite anyone in the research community to use the OpenArm and OpenArm Multisensor data sets to validate existing muscle deformation models or to devise new ones.
Full details can be found in the following papers:
Laura A. Hallock, Bhavna Sud, Chris Mitchell, Eric Hu, Fayyaz Ahamed, Akash Velu, Amanda Schwartz, and Ruzena Bajcsy. "Toward Real-Time Muscle Force Inference and Device Control via Optical-Flow-Tracked Muscle Deformation." In IEEE Transactions on Neural Systems and Rehabilitation Engineering (TNSRE). IEEE, 2021. (Under review.)
Laura Hallock, Akash Velu, Amanda Schwartz, and Ruzena Bajcsy. "Muscle deformation correlates with output force during isometric contraction." In IEEE RAS/EMBS International Conference on Biomedical Robotics & Biomechatronics (BioRob). IEEE, 2020. (Available at https://people.eecs.berkeley.edu/~lhallock/publication/hallock2020biorob.)
Yonatan Nozik*, Laura A. Hallock*, Daniel Ho, Sai Mandava, Chris Mitchell, Thomas Hui Li, and Ruzena Bajcsy, "OpenArm 2.0: Automated Segmentation of 3D Tissue Structures for Multi-Subject Study of Muscle Deformation Dynamics," in International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), IEEE, 2019. *Equal contribution. (Available at https://people.eecs.berkeley.edu/~lhallock/publication/nozikhallock2019embc.)
Laura Hallock, Akira Kato, and Ruzena Bajcsy. "Empirical quantification and modeling of muscle deformation: Toward ultrasound-driven assistive device control." In IEEE International Conference on Robotics and Automation (ICRA). IEEE, 2018. (Available at https://people.eecs.berkeley.edu/~lhallock/publication/hallock2018icra.)
This project is currently in development in the Human-Assistive Robotic Technologies (HART) Lab at the University of California, Berkeley (http://hart.berkeley.edu). | |
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Registered: 2018-11-28 20:40 |
Are subject-specific musculoskeletal models robust to parameter identification?
- This study analyzed the sensitivity of the predictions of an MRI-based musculoskeletal model (i.e., joint angles, joint moments, muscle and joint contact forces) during walking to the unavoidable uncertainties in parameter identification, i.e., body landmark positions, maximum muscle tension and musculotendon geometry. To this aim, we created an MRI-based musculoskeletal model of the lower limbs, defined as a 7-segment, 10-degree-of-freedom articulated linkage, actuated by 84 musculotendon units. We then performed a Monte-Carlo probabilistic analysis perturbing model parameters according to their uncertainty, and solving a typical inverse dynamics and static optimization problem using 500 models that included the different sets of perturbed variable values. Model creation and gait simulations were performed by using freely available software that we developed to standardize the process of model creation, integrate with OpenSim and create probabilistic simulations of movement. | |
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Activity Percentile: 93.13 Registered: 2014-11-10 15:19 |
Predicting Cell Deformation from Body Level Mechanical Loads
- This project is a NIBIB/NIH funded study (1R01EB009643-01) to establish models and computational platforms to predict cellular deformations from joint level mechanical loading.
Collaborators:
Ahmet Erdemir (PI), Amit Vasanji, Jason Halloran (Cleveland Clinic)
Cees Oomens, Frank Baaijens (Eindhoven University of Technology)
Jeff Weiss (University of Utah)
Farshid Guilak (Duke University)
Summary (from grant proposal):
Cells of the musculoskeletal system are known to have a biological response to deformation. Deformations, when abnormal in magnitude, duration, and/or frequency content, can lead to cell damage and possible disruption in homeostasis of the extracellular matrix. These mechanisms can be studied in an isolated fashion but connecting mechanical cellular response to organ level mechanics and human movement requires a multiscale approach. At the organ level, physicians perform surgical procedures, investigators try to understand risk of injury, and clinicians prescribe preventive and therapeutic interventions. Many of these operations are aimed at management and prevention of cell damage, and to associate joint level mechanical markers of failure to cell level failure mechanisms. Through human movement, one explores neuromuscular control mechanisms and the influence of physical activity on musculoskeletal tissue properties. At a lower level, mechanical sensation of cell deformations regulate movement control. Physical rehabilitation and exercise regimens are prescribed to promote tissue healing and/or strengthening through cellular regeneration. The knowledge of the mechanical pathway, through which the body level loads are distributed between organs, then within the tissues and further along the extracellular matrix and the cells, is critical for the success of various interventions. However, this information is not established. The goal of this research proposal is to portray that prediction of cell deformations from loads acting on the human body, therefore a clear depiction of the mechanical pathway, is possible, if a multiscale simulation approach is used. Multiresolution models of the knee joint, representative of joint, tissue and cell structure and mechanics, will be developed for this purpose. The knee endures high rates of traumatic injury to its soft tissue structures and it is predominantly affected by osteoarthritis, chronically induced by abnormalities in mechanical loading or how it is transferred to the cartilage. Through multiscale mechanical coupling of these models, a map of cellular deformation in cartilage, ligaments and menisci under a variety of tibiofemoral joint loads will be obtained. Comprehensive mechanical testing at joint, tissue and cell levels will be conducted for parameter estimation and validation, including in vitro loading of the knee joint representative of lifelike loading scenarios. In addition, imaging modalities will capture joint and tissue anatomy, and spatial and deformation related information from cell and extracellular matrix. Advanced computational approaches will be used to obtain model properties and to facilitate multiscale simulations. The approach will combine the expertise of many investigators experienced in biomechanical modeling and experimentation at various biological scales, some with clinical expertise. In future, the research team will utilize this platform to establish the relationship between the structural and loading state of the knee and chondrocyte stresses to explore potential mechanisms of cartilage degeneration. Through documented dissemination of data and models, simulations of other pathologies and translation of the methodology to other organs can be carried out by any interested investigator. | |
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Registered: 2009-07-23 17:33 |
Model of the Scapulothoracic Joint
- In this study, we developed a rigid-body model of a scapulothoracic joint to describe the kinematics of the scapula relative to the thorax. This model describes scapula kinematics with four degrees of freedom: 1) elevation and 2) abduction of the scapula on an ellipsoidal thoracic surface, 3) upward rotation of the scapula normal to the thoracic surface, and 4) internal rotation of the scapula to lift the medial border of the scapula off the surface of the thorax. The surface dimensions and joint axes can be customized to match an individual’s anthropometry. We compared the model to “gold standard” bone-pin kinematics collected during three shoulder tasks and found modeled scapula kinematics to be accurate to within 2 mm root-mean-squared error for individual bone-pin markers across all markers and movement tasks. As an additional test, we added random and systematic noise to the bone-pin marker data and found that the model reduced kinematic variability due to noise by 65% compared to Euler angles computed without the model. Our scapulothoracic joint model can be used for inverse and forward dynamics analyses and to compute joint reaction loads. The computational performance of the scapulothoracic joint model is well suited for real-time applications, is freely available as an OpenSim 3.2 plugin, and is customizable and usable with other OpenSim models. | |
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Activity Percentile: 88.55 Registered: 2015-01-14 23:10 |
BlurLab -- 3D Microscopy Simulation Package
- BlurLab is an easy to use platform for generating simulated fluorescence microscopy data for use in mechanistic modeling visualization, image comparison, and hypothesis testing. The software accepts the 3D positions, intensities and labels of fluorescing objects that are produced by an underlying mechanistic model and transforms them into high quality simulated images. The program includes full 3D convolution with realistic (or even measured) point spread functions; inclusion of thermal, shot and custom noise spectra; simulations of mean and fully stochastic photobleacing; the ability to view scenes in wide-field and TIRF, and perform Z-slicing; and the ability to simulate FRAP experiments.
The software provides a platform for adjusting and saving these simulated images, as well as a number of helpful, semi-automated features to make image simulation easy and less error prone. | |
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Activity Percentile: 80.15 Registered: 2011-08-05 01:17 |
Matlab MOtion data elaboration TOolbox for NeuroMusculoSkeletal apps (MOtoNMS)
- MOtoNMS processes experimental data from C3D files of different motion analysis devices and produces input data for OpenSim (.trc and .mot, OpenSim file formats). When available, EMG signals are also processed and can be exported in several formats (.mot, OpenSim motion, .sto, OpenSim Storage, and .txt, plain text format) compatible with the CEINMS toolbox (https://simtk.org/home/ceinms), and easily usable also by other applications.
Procedures implemented in MOtoNMS include: (i) computation of centers of pressure and torques for the most commonly available force platforms (types from 1 to 4, including Bertec, AMTI and Kistler); (ii) rotation of motion capture data between different coordinate systems (those of force platforms, laboratory and OpenSim); (iii) EMG filtering, maximum peak computation, and normalization; (iv) exportation of data ready to be used in OpenSim and CEINMS toolbox. Procedures are highly configurable through user-friendly graphical interfaces that setup XML files listing all the parameters of the execution.
The architecture has been designed to easily accommodate new contributions in instrumentations, protocols, and methodologies. Additionally, data management results in a clear organization of input data and an automatic generation of output directories with a uniquely defined structure.
The tool has been already tested on data from several laboratories with different instruments and procedures for the data collection.
MOtoNMS is released under GNU General Public Licence and freely available to the community without warranty. The software requires either Motion Labs C3D Server software or BTK (Biomechanical ToolKit).
A manual is included with the software, while a html version is always available from the GitHub Project Pages at http://rehabenggroup.github.io/MOtoNMS/. For doubts, suggestions, bugs please either use the MOtoNMS forum or send us an email. This is an ongoing project, any feedback is really appreciated.
When using MOtoNMS or our Test Data, please acknowledge the authors and cite our main publication:
Mantoan et al. Source Code for Biology and Medicine (2015) 10:12
DOI 10.1186/s13029-015-0044-4
http://www.scfbm.org/content/10/1/12 | |
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Activity Percentile: 75.57 Registered: 2014-02-16 11:33 |
Convert .c3d and .csv files to OpenSim files without any program but MatLab
- This project is a series of routines that allows a OpenSim user with little programing skills to convert their own .c3d and .csv files with biomechanical experimental data into OpenSim .trc and .mot files. | |
Activity Percentile: 75.19 Registered: 2015-06-05 18:12 |
SAFA Footprinting Software
- Quantitative analysis of gels from hydroxyl radical footprinting and other structure mapping techniques can provide a great deal of insight into the structural details of RNA molecules. We have developed and implemented a software package (SAFA v1.1) that allows rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, we estimate that an entire gel with thousands of bands can be quantified in less than 10 minutes. In general all the automated features have amanual override, such that even difficult or exceptional gels can be analyzed with the package. | |
Activity Percentile: 72.90 Registered: 2005-10-27 17:03 |
Batch OpenSim Processing Scripts (BOPS)
- BOPS performs batch processing of common OpenSim procedures (Inverse Kinematics - IK, Inverse Dynamics - ID, Muscle Analysis - MA, Static Optimization - SO, and Joint Reaction Analysis - JRA) and stores output, logging information, setup files, and plots in an ordered structure of folders.
We implemented BOPS using OpenSim APIs, that receive the following information through setup files: (i) name and weight of each marker (IK); (ii) external loads (ID); (iii) muscles and moment arms of interest (MA); (iv) static optimization conditions, and muscle actuators loads (SO); (v) joints of interest (JRA). The user is in charge of defining the appropriate configuration for its data, but we already provide several templates for each setup file to speed up their customization.
A MATLAB Graphical User Interface (GUI) is available to simplify the execution of procedures. The use of the GUI is not limited to inputting the setup files. The user can also select: (i) the OpenSim procedures to execute, (ii) the trials to process, (iii) the OpenSim model to use on the simulations, (iv) the cut-off frequencies for the filtering, (v) the residual actuators, (vi) the output variables to plot and the x-axis label.
The software only requires to configure MATLAB for the use of OpenSim API (http://simtk-confluence.stanford.edu:8080/display/OpenSim/Scripting+with+Matlab), and it is based on the data folder organization provided by MOtoNMS software (https://simtk.org/home/motonms).
BOPS stores its outputs in folders that are automatically created and that integrate perfectly in the structure provided by MOtoNMS software (https://simtk.org/home/motonms). We designed the two tools to work in close cooperation to transform the data collected in a motion analysis laboratory into inputs for OpenSim and CEINMS (https://simtk.org/home/ceinms) tools.
BOPS is released under Apache v2.0 License and freely available to the community without warranty. Latest updates can be found on the GitHub repository (https://github.com/RehabEngGroup/BOPS).
Thanks to the recent join of the Human Movement Biomechanics Laboratory (University of Ottawa, Canada) to the project, the tool has been refined and extensively tested on data from several laboratories and with different combinations of procedures, setups and user choices. Their precious contribution has allowed also the addition of the JRA procedure to those already available and led to the release of v2.0, a definitely improved and more stable version.
A tutorial video exemplifying how to use BOPS v2.0 is available in the Documents section.
For any doubts, suggestions, bugs please either use the BOPS forum or send us an email.
This is an ongoing project, therefore any feedback is really appreciated.
When using BOPS or our Test Data, please acknowledge the authors and cite our main publication:
Bruno L. S. Bedo, Alice Mantoan, Danilo S. Catelli, Willian Cruaud, Monica Reggiani & Mario Lamontagne (2021): BOPS: a Matlab toolbox to batch musculoskeletal data processing for OpenSim, Computer Methods in Biomechanics and Biomedical Engineering
DOI: 10.1080/10255842.2020.1867978 | |
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Activity Percentile: 71.76 Registered: 2015-09-05 18:12 |
DireX - Conformational Sampling under Low Resolution Restraints
- This project provides a tool for efficient conformational sampling of protein structures under low resolution restraints. Low resolution electron density maps obtained from, e.g., electron microscopy, as well as distance restraints obtained from NMR or FRET experiments can be used to guide the sampling. | |
Activity Percentile: 67.94 Registered: 2007-03-07 20:47 |
Musculoskeletal Representation of Large Repertoires of Hand Grasping in Primates
- The project aims to investigate and characterize the complex function of the primate hand at the musculoskeletal level. The OpenSim models used in this project enabled extracting joint angles from 27 degrees of freedom as well as length of 50 musculotendon units in the hand and upper extremity. Results demonstrated both a more compact representation and a higher decoding capacity of grasping tasks when movements were expressed in the muscle kinematics domain than when expressed in the joint kinematics domain. The OpenSim models in the project were adapted from the upper extremity model by Holzbaur et al., Ann.Biomed. Eng., 2005. | |
Activity Percentile: 66.41 Registered: 2015-02-10 15:59 |
Calibrated EMG-Informed Neuromusculoskeletal Modelling Toolbox (CEINMS)
- The software permits the simulation of all the transformations that take place from the onset of muscle excitation to the generation of force in 34 musculotendon units and the resulting moments about six degrees of freedom (DOFs) in the lower extremity. The selected DOFs include: hip flexion-extension, hip adduction-abduction, hip internal-external rotation, knee flexion-extension, ankle plantar-dorsi flexion, and ankle subtalar angle.
Experimentally recorded electromyography (EMG) signals and three-dimensional joint angles can be used to determine the neural drive and the instantaneous kinematics for the multiple musculotendon units being modelled. Furthermore, the CEINMS software can estimate the excitation patterns for musculotendon units from which EMGs cannot be experimentally measured and adjust the EMG linear envelopes that may be subject to measurement errors and uncertainties, while ensuring dynamical consistency in the predicted joint moments.
Finally, the CEINMS software allows automatically identification of a number of parameters that determine the way musculotendon units activate and contract, which vary non-linearly across individuals. This is done via an optimization-based calibration procedure that adjusts the internal parameters to best reflect the anatomy and physiology of an individual. | |
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Activity Percentile: 66.03 Registered: 2013-02-19 05:59 |
Interaction Between Biology and Robotics
- In this project we study a salient feature of human motor skill learning that is the ability to exploit similarities across related tasks. We test this concept in forward dynamics simulations of multiple reaching movements of a musculoskeletal arm model with eleven muscles. The eleven muscle activation patterns are generated by a combination of parametrized muscle synergies, where these synergies encode a shared prior among multiple reaching directions. | |
Activity Percentile: 65.65 Registered: 2013-10-11 11:51 |
Cervical Spine Injury Mechanisms Analysis and Simulation in Sport
- This project provides the following models:
1) MASI: full body model for the analysis of cervical spine loading during a various set of activities. The MASI is an in-silico representation of a healthy subject, and includes:
a) a custom joint that allows scapula and clavicle coupled motion with respect to humeral elevation;
b) full body inertial parameters for dynamic analyses;
c) neck kinematics from Vasavada Head&Neck model
d) optimised neck muscle parameters representative of a healthy subject's neck strength.
2) THE RUGBY MODEL: this is rugby-specify version of the MASI, and was created to estimate cervical spine load in rugby activities and other sports impacts involving upper body contacts. It includes the same characteristics of the MASI model, but the inertial properties were changed and informed by a DEXA scan of a front row rugby player;
The previous model versions can be used for inverse analysis and simulations in order to estimate cervical spine internal loading during non-injurious scenarios.
3) THE RUGBY MODEL + IMPACT SPECIFIC BUSHING PARAMETERS: This updated version of The Rugby Model includes viscoelastic bushing elements implemented at the C2-C3 to C5-C6 joints validated for axial impacts (Silvestros et al., 2019) [10.1371/journal.pone.0216663]. This model can be used for forward simulation to explore cervical spine loading and injury mechanisms doing injurious events.
4) THE RUGBY MODEL + MRI-informed MUSCLE PARAMETERS: This updated version of The Rugby Model includes wrapping surfaces and updated muscle parameters, and can be used to calculate muscle lengths and moment arms, as well as the forces and moments around the cervical spine during non-injurious scenarios. | |
Activity Percentile: 61.45 Registered: 2015-01-02 16:19 |
Studying Anterior Cruciate Ligament Strains in Young Female Athletes
- The central goal of this study is to contribute toward advancements made in determining the underlying causes of anterior cruciate ligament (ACL) injuries in young female athletes performing high impact activities like stop jumps. ACL injuries are frequently incurred by recreational and professional young female athletes during non-contact impact activities in sports like volleyball and basketball. This musculoskeletal-neuromuscular study investigated stop jumps and factors related to ACL injury like knee valgus and internal–external rotations and moment loads, as well as ACL strains and internal forces. The dynamic simulation steps undertaken for this analysis using OpenSim 3.2 include Model Scaling, Inverse Kinematics, Residual Reduction, Computed Muscle Control and Forward Dynamics. | |
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Activity Percentile: 58.40 Registered: 2014-08-05 18:24 |
Tim's OpenSim Utilities
- This project site is concerned with extending the functionality of OpenSim through the use of scripting tools and plugins.
Click on the downloads link to browse the set of freely available OpenSim tools for download.
*******************************************************
Previously delivered interactive webinars demonstrating
the use of the Pseudo-Inverse Induced Acceleration
plugin for OpenSim (IndAccPI).
http://www.stanford.edu/group/opensim/support/webinars.html
******************************************************* | |
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Registered: 2009-09-01 00:52 |
Analysis of arm swing during human walking
- This project provides a simplified version of the UpperLowerBodySimple model from the ULB-project, which was adjusted with the purpose to decrease the run time of the simulations.
The adjusted model was used to determine arm swing kinematics (with and without muscle excitations) during human walking, with arm movements not exceeding 70 degrees of anteflexion or abduction. However, the adjusted_ULB model can be used for modeling and simulating kinematics and kinetics of all neuromusculoskeletal systems.
For an example of an arm swing simulation without muscle excitation we refer to the video below.
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Activity Percentile: 56.49 Registered: 2013-10-19 09:43 |
HiTRACE: High-Throughput Robust Analysis for Capillary Electrophoresis
- This project contains the HiTRACE software that allows users to accurately and automatically perform key quantitative analysis tasks involved in high-throughput capillary electrophoresis (CE) of nucleic acids. CE has become a workhorse technology underlying high-throughput experimental methods such as high-speed genome sequencing and large-scale footprinting for nucleic acid structural inference. Despite the wide availability of CE-based equipment, there remain challenges in leveraging the full power of CE for quantitative analysis of RNA and DNA structure. We developed HiTRACE in order to address this issue. See <a href="http://arxiv.org/abs/1104.4337">Preprint</a> for more information. | |
Activity Percentile: 51.53 Registered: 2010-11-10 08:11 |
C3D Extraction Toolbox
- This toolbox is of benefit to musculoskeletal modellers in the field of biomechanics / bioengineering to assist extracting kinematic, kinetic, and EMG information directly from a C3D file for Matlab manipulation or for input to OpenSim biosimulation software. The scripts can be configured for any laboratory configuration. This software is free without warranty but I do ask for acknowledgement if used in publications. Free download is available with documentation and two examples included.
Main features of this script include:
Custom markerset extraction
Foot-plate detection algorithm
Kinetic extraction (ground reaction forces / moments)
Center of pressure calculation
Transformation to customizable model coordinate system
Custom EMG acquisition & processing tools
XML file production (for OpenSim)
Lab customizable
The scripts require Motion Labs C3D Server software (freeware) and XML Toolbox (Marc Molinari)(freeware) which is included with the script download. Also requires Matlab 2008 or greater (32 bit only) with the Signal Processing Toolbox.
Additional C3D software may be useful and these are available at http://www.c3d.org/c3dapps.html. Review the included manual for version updates and additions. Please inform me of bugs / suggestions to improve as this will be an ongoing project. | |
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Registered: 2008-10-03 01:17 |
A predictive model of muscle excitations based on muscle modularity
- Humans can efficiently walk across a large variety of terrains and locomotion conditions with little or no mental effort. It has been hypothesized that the nervous system simplifies neuromuscular control by using muscle synergies, thus organizing multi-muscle activity into a small number of coordinative co-activation modules. With this project we want to investigate how muscle modularity is structured across a large repertoire of locomotion conditions including five different speeds and five different ground elevations. For this we have used the non-negative matrix factorization technique in order to explain EMG experimental data with a low-dimensional set of four motor components. This descriptive analysis was translated into a predictive model that could: 1) Estimate how motor components modulate across locomotion speeds and ground elevations. This implies not only estimating the non-negative factors temporal characteristics, but also the associated muscle weighting variations. 2) Estimate how the resulting muscle excitations modulate across novel locomotion conditions and subjects. | |
Activity Percentile: 35.88 Registered: 2015-08-12 06:11 |
44 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3>