- Opensim-announcement - SimTK Mailing Lists

Virtual Office Hours Applications, Tool for Automatic Generation of Personalized Models, Biomechanics Class Resources
by Joy P. Ku 15 Mar '21

15 Mar '21

Apply to Participate in Virtual Office Hours for Biomechanical Modeling or Machine Learning Research Questions Applications due: April 9, 2021, 5 PM local time Meeting dates: Weeks of April 19 and April 26, 2021 We are pleased to announce our April Virtual Office Hours to support researchers working with wearable sensors, video technology, and other modalities in rehabilitation research. These office hours are offered as part of the training efforts of our Restore<https://restore.stanford.edu/> and Mobilize<https://mobilize.stanford.edu/> Centers. We will have two tracks: 1) Biomechanical modeling with OpenSim<https://opensim.stanford.edu/> and IMUs<https://simtk-confluence.stanford.edu/display/OpenSim/OpenSense+-+Kinematic…> or video, and 2) Machine learning, including video analysis. All phases of a research project are supported, such as formulating a research question, choosing and planning appropriate methods, and addressing issues with carrying out the study. We welcome and encourage individuals to apply as a team, if applicable. Learn more and apply<https://mobilize.stanford.edu/2021/03/12/apply-to-participate-in-virtual-of…> MATLAB Toolbox for Automatic Generation of Personalized OpenSim Models Luca Modenese from Imperial College London and Jean-Baptiste Renault from Aix-Marseille University have recently released STAPLE (Shared Tools for Automatic Personalized Lower Extremity modeling), a MATLAB toolbox to automatically create kinematic and kinetic models of the lower extremity using subject-specific bone geometries segmented from medical images. Numerous examples of use and testing datasets are available. Read publication<https://www.sciencedirect.com/science/article/pii/S0021929020306102?via%3Di…> | Download stable release<https://simtk.org/projects/msk-staple> | Access code development via GitHub <https://github.com/modenaxe/msk-STAPLE> Resources Available for OpenSim-Based Class Project and Jeopardy!-Inspired Exam Review The Biomechanics of Movement textbook's Classroom site<https://simtk-confluence-homeworks.stanford.edu/pages/viewpage.action?pageI…> hosts homework problems and other materials for teaching biomechanics. This includes a number of OpenSim-related resources. The site has just made available: * A Jeopardy!-inspired exam review for an advanced undergrad/early grad student course in biomechanics, from Kat Steele at University of Washington * Materials for a class project that guides students through two different approaches for using OpenSim to predict in vivo medial and lateral knee contact forces, from B.J. Fregly at Rice University. Included are instructions, experimental data, setup files, the OpenSim model, and a grading rubric. These two resources are available to instructors only, but the site's collection of homework problems<https://simtk-confluence-homeworks.stanford.edu/display/BMH/Homework+Proble…> are available to students and instructors. Join educator/instructor community<https://biomech.stanford.edu/contribute/> | Access instructor resources<https://simtk-confluence-homeworks.stanford.edu/display/BMH/Contributions> -- Joy P. Ku, PhD Project Manager | SimTK<https://simtk.org/> Director of Communications and Engagement | Mobilize Center<https://mobilize.stanford.edu/> Director of Promotions and Didactic Interactions | Restore Center<https://restore.stanford.edu/> Director of Communications and Training | NCSRR<https://opensim.stanford.edu/> Stanford University 650.736.8434 | joyku(a)stanford.edu

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Webinar on movement analysis with videos, biomechanics textbook, postdoc opening, batch processing toolbox
by Joy P. Ku 28 Jan '21

28 Jan '21

Webinar: Quantitative Movement Analysis Using Single-camera Videos February 9, 2021, at 10:00 a.m. Pacific Time The Mobilize Center<https://mobilize.stanford.edu/> is launching their webinar series featuring Lukasz Kidzinski from Stanford University presenting "Quantitative Movement Analysis Using Single-camera Videos". In the first half of this webinar, he will present our findings from analyzing a dataset of 1700+ videos of patients from Gillette Children's Specialty Healthcare. The second half of the webinar will be a short hands-on tutorial aimed at getting individuals started on running deep learning algorithms in the cloud to analyze movement from a single-camera video. Register now<https://mobilize.stanford.edu/2021/01/21/mobilize-webinar-quantitative-move…> "Biomechanics of Movement" Textbook and Online Resources We are pleased to announce the publication of the "Biomechanics of Movement: The Science of Sports, Robotics, and Rehabilitation" textbook, authored by Scott Delp and Thomas Uchida. The book describes foundational biological and physics-based concepts that have been used to analyze movement. It also guides readers in the use of modeling and simulation for understanding movement and is accompanied by online resources, including homework problems, models, and data. Explore the resources and the book<https://biomech.stanford.edu/> MATLAB Toolbox to Batch Process Data for OpenSim Bruno Bedo from University of Ottawa and colleagues have released BOPS, an open-source MATLAB toolbox for batch processing common OpenSim procedures, such as inverse kinematics and joint reaction analysis. It provides a graphical user interface for customizing the workflow. BOPS is described in more detail in a recent publication in Computer Methods in Biomechanics and Biomedical Engineering. Read more<https://www.tandfonline.com/doi/abs/10.1080/10255842.2020.1867978> | Access BOP<https://simtk.org/projects/bops> Opening for Digital Human Modeling Postdoctoral Fellowships at Stanford University A team of faculty at Stanford University, including Professors Scott Delp, Garry Gold, Karen Liu, Akshay Chaudhari, Ellen Kuhl, Oussama Khatib, Fei Fei Li, and Serena Yeung is accepting applications for several Postdoctoral Fellows in digital human modeling. Individuals with backgrounds in biomechanics, neuroscience, biomedical imaging, biomedical informatics, robotics, and computer science are all welcome to apply. We are searching for outstanding individuals to join our team and develop new methods to simulate and analyze human movement. Our interdisciplinary approach will leverage novel data sources, such as real-world wearable sensors and video, advanced biomedical imaging, multi-scale modeling, and state-of-the-art models of neural control. Learn more and apply<https://nmbl.stanford.edu/opportunities/postdoctoral-fellowships-in-digital…> -- Joy P. Ku, PhD Project Manager | SimTK<https://simtk.org/> Director of Communications and Engagement | Mobilize Center<https://mobilize.stanford.edu/> Director of Promotions and Didactic Interactions | Restore Center<https://restore.stanford.edu/> Director of Communications and Training | NCSRR<https://opensim.stanford.edu/> Stanford University 650.736.8434 | joyku(a)stanford.edu

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Consultations Available for Biomechanical Modeling or Machine Learning Questions
by Joy P. Ku 16 Dec '20

16 Dec '20

Consultations Available for Biomechanical Modeling or Machine Learning Questions The Mobilize Center<https://mobilize.stanford.edu/> and the Restore Center<https://restore.stanford.edu/> are offering a Virtual Office Hours program to support researchers working with wearable sensors, video technology, and other modalities in rehabilitation research. Researchers can apply for 30-minute consultations in one of two tracks: 1) Biomechanical modeling with OpenSim<https://opensim.stanford.edu/> and/or inertial measurement units (IMUs<https://simtk-confluence.stanford.edu/display/OpenSim/OpenSense+-+Kinematic…>), and 2) Machine learning, including video analysis. All phases of a research project are supported, such as formulating a research question, choosing and planning appropriate methods, and addressing issues with carrying out the study. Application deadline: January 8, 2021. Learn more<https://mobilize.stanford.edu/2020/12/11/apply-to-participate-in-virtual-of…> -- Joy P. Ku, PhD Project Manager | SimTK<https://simtk.org/> Director of Communications and Engagement | Mobilize Center<https://mobilize.stanford.edu/> Director of Promotions and Didactic Interactions | Restore Center<https://restore.stanford.edu/> Director of Communications and Training | NCSRR<https://opensim.stanford.edu/> Stanford University 650.736.8434 | joyku(a)stanford.edu

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Mobilize Center, Beta Testing for OpenSim 4.2, and more
by Joy P. Ku 09 Dec '20

09 Dec '20

Mobilize Center to Serve as an NIBIB Biomedical Technology Resource Center and Continue Development of OpenSim Software We are pleased to announce that the Mobilize Center, led by Scott Delp, has been awarded a Biomedical Technology Resource Center (BTRC) grant from the National Institutes of Health's National Institute of Biomedical Imaging and Bioengineering (NIBIB). As a BTRC, the Center will provide tools and training to help researchers utilize wearable sensors, video, medical images, and other data sources to quantify movement biomechanics, extract insights about conditions that reduce mobility, and advance precision rehabilitation. This includes development of OpenSense, software for wearable-based biomechanics which has been integrated into OpenSim 4.1, and continued development of OpenSim and OpenSim Moco to support biomechanical modeling for these new applications. Learn more<https://mobilize.stanford.edu/> Sign up to be a Beta Tester We are ramping up for the release of OpenSim 4.2, which will include a tool in the OpenSim Mac and Windows application (GUI) to perform inverse kinematics with inertial measurement units (IMU) orientation data, improved integration with Moco, and more. Sign up to be a beta tester<https://lists.simtk.org/mailman/listinfo/opensim-testers> and get early access to these new features. New Approach for Estimating Muscle Forces and Activations Using Synergies Mohammad Shourijeh and B.J. Fregly from Rice University have developed a novel approach called Synergy Optimization (SynO), which estimates muscle forces and activations in a way that may reduce indeterminacy and improve physiological co-activation compared with static optimization. It uses synergy activations and their associated synergy vectors as design variables within the optimization framework. Read the paper<https://www.semanticscholar.org/paper/Muscle-Synergies-Modify-Optimization-…> | Download the simulation scripts and experimental data<https://simtk.org/projects/syno> Postdoc/Project Scientist Openings for Individuals with Expertise in Computational Biomechanics and Mechanobiology The Institute for Engineering in Medicine at UC San Diego is recruiting for one or more post-doctoral scholars or project scientists with expertise in computational biomechanics and mechanobiology to develop integrative multi-scale models of tissues. The successful candidate will be part of an interdisciplinary team with expertise in experimental and computational biomechanics and mechanobiology, systems biology, tissue engineering and physiology. Strong communication and organizational skills, expertise in software development and numerical methods, and familiarity with major open-source software tools in the field such as OpenSim and FEBio are preferred. Learn more and apply<https://simtk.org/opportunities.php#job1> -- Joy P. Ku, PhD Project Manager | SimTK<https://simtk.org/> Director of Communications and Engagement | Mobilize Center<https://mobilize.stanford.edu/> Director of Promotions and Didactic Interactions | Restore Center<https://restore.stanford.edu/> Director of Communications and Training | NCSRR<https://opensim.stanford.edu/> Stanford University 650.736.8434 | joyku(a)stanford.edu

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Pilot Project Updates, New Resources, and New OpenSim Fellow
by Jen Hicks 11 Sep '20

11 Sep '20

*Updated Eligibility Criteria for Restore Center Pilot Project Applications* The Restore Center <http://restore.stanford.edu/> at Stanford University seeks proposals for innovative and meritorious projects that will accelerate the use of sensor and video technology in rehabilitation research and will advance real-world monitoring and delivery of medical rehabilitation for individuals with impaired movement. Applicants can request up to $30,000 in funding. Applications are due on October 1, 2020. The eligibility criteria for applying to this program has recently been changed based on guidance from the NIH. Among other changes, the program is now limited to individuals from U.S. institutions. Read more and learn about other changes <https://restore.stanford.edu/pilot-funding>. *New Resource to Guide the Use of OpenSim in Research* As the capabilities of OpenSim have expanded and the interests of the research community have broadened, we know that it can be challenging to decide what OpenSim workflow is most appropriate for a given research question. In response, we have recently updated our documentation to better describe the different pipelines and tools for simulation available in OpenSim. You can read this Overview of OpenSim Workflows <https://simtk-confluence.stanford.edu/display/OpenSim/Overview+of+OpenSim+W…> and also watch the accompanying webinar <https://www.youtube.com/watch?v=e0gfkm5_Rps&feature=youtu.be>. *Gil Serrancolí Masferrer Becomes Newest OpenSim Fellow* Congratulations to Dr. Serrancolí on becoming the newest OpenSim Fellow. Dr. Serrancolí is an Assistant Professor of Mechanical Engineering at the Universitat Politècnica de Catalunya. He is an expert on knee modeling and optimization approaches for musculoskeletal simulation. This honor recognizes a strong commitment to the OpenSim community and a deep expertise in biomechanical modeling and simulation. Read more about the current fellows <https://simtk-confluence.stanford.edu/display/OpenSim/OpenSim+Fellows> and learn how to apply <https://opensim.stanford.edu/support/fellows.html>.

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Announcing the Restore Center and a Pilot Funding Opportunity
by Scott L Delp 17 Aug '20

17 Aug '20

We are pleased to announce the launch of the Restore Center<http://restore.stanford.edu/>, an NIH-funded center whose mission is to create a worldwide collaboration to gain insights from real-world data on rehabilitation outcomes. You can read more about the Center’s services and our call for pilot project applications below. To get updates on the Restore Center’s activities, be sure to sign up for the mailing list<https://mailchi.mp/176a9dc1d8ba/the-restore-center>, which is separate from this OpenSim mailing list. You can also follow the Center on Twitter at @restore_center. Thank you to everyone who provided letters of support for our funding application last year. We look forward to continuing our work with the OpenSim community and beyond through this new Center. The Restore Center and OpenSim teams Introducing the Restore Center The Restore Center is one of six centers in the Medical Rehabilitation Research Resource (MR3) Network. Funded by the National Institute of Child Health & Human Development (NICHD) and the National Institute of Neurological Disorders and Stroke (NINDS), the Restore Center will provide vital infrastructure and training to accelerate research using mobile sensor and video technology for real-word monitoring in rehabilitation, including: * Easy-to-use software workflows for rehabilitation researchers to estimate common real-world outcome measures * A pilot project program to fund promising investigators * A fellows program to create hubs of expertise around the country and world * Scientific challenges to foster collaboration between rehabilitation researchers and experts from other domains, such as machine learning and robotics * Online training materials, such as best practice guides and software documentation * Training opportunities, such as multi-day, in-person training workshops and virtual office hours Learn more<http://restore.stanford.edu/> Apply for a Restore Center Pilot Project Grant Up to $30,000 Applications due October 1, 2020 The Restore Center at Stanford seeks proposals for our pilot project program. The program awards seed grants to innovative and meritorious projects that will accelerate the use of sensor and video technology in rehabilitation research and will advance real-world monitoring and delivery of medical rehabilitation. Applicants can request up to $30,000 in funding. Learn more and apply<https://restore.stanford.edu/pilot-funding> Scott L. Delp James H. Clark Professor Schools of Engineering and Medicine Stanford University http://mobilize.stanford.edu<http://mobilize.stanford.edu/> http://opensim.stanford.edu<http://opensim.stanford.edu/> http://www.stanford.edu/group/nmbl

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Webinar on "Inverse Kinematics: A Bayesian Versus Least-Squares Approach"
by Joy P. Ku 08 Jul '20

08 Jul '20

Join Our Next Webinar "Inverse Kinematics: A Bayesian Versus Least-Squares Approach" Monday, July 20, 2020 at 4:00pm PDT We invite you to join us for a webinar featuring Todd Pataky from Kyoto University. In this webinar, Dr. Pataky will introduce you to Bayesian statistics and demonstrate how it can be used for estimating joint kinematics from a set of noisy marker measurements, a process commonly referred to as inverse kinematics. He will compare the Bayesian approach to the least-squares approach which is traditionally used in inverse kinematics. Learn more and register<https://stanford.webex.com/mw3300/mywebex/default.do?nomenu=true&siteurl=st…> --- Joy P. Ku, PhD Project Manager, SimTK<http://simtk.org/> Director of Communications & Training, NCSRR<http://opensim.stanford.edu/> Director of Communications & Engagement, Mobilize Center<http://mobilize.stanford.edu/> Stanford University (w) 650.736.8434 Email: joyku(a)stanford.edu<mailto:joyku@stanford.edu>

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Webinar on OpenSim via Matlab plus New Tutorial and Resources
by Jennifer Hicks 24 Jun '20

24 Jun '20

*Join Our Next Webinar "Automating OpenSim Workflows: An Intro to the OpenSim API in Matlab"* *July 7, 2020 at 10:00am PDT* We invite you to join us for a webinar featuring Christopher Dembia from Stanford University. In this webinar, Dr. Dembia from the OpenSim development team will introduce you to OpenSim’s Application Programming Interface (API) in Matlab, starting from the very basics. He will discuss how to build a point-mass model, simulate it, and then analyze the simulation. He will also discuss key concepts, such as the difference between a Model and its State. For the hour following the webinar, those interested in trying the example for themselves can participate in virtual office hours. Anyone interested in this (optional) part of the webinar should set-up OpenSim for Matlab <https://simtk-confluence.stanford.edu/display/OpenSim/Scripting+with+Matlab…> before the webinar. Learn more and register <https://stanford.webex.com/stanford/onstage/g.php?MTID=ef0292aee60cb5c3000e…> . *Learn About the OpenSim API and Static Optimization with a New Example* We recently created a new example that guides you through the process of writing your own code to perform static optimization in Matlab via the OpenSim API. The development of this new example was led by Nick Bianco, a PhD student at Stanford University. By working through this lab, you will learn the basics of the static optimization problem, become familiar with using the OpenSim API through MATLAB, and learn how to write your own static optimization code. Try the new example <https://simtk-confluence.stanford.edu/display/OpenSim/Custom+Static+Optimiz…> . *Using Pre-Operative Gastrocnemius Lengths to Predict Outcomes of Gastrocnemius Lengthening Surgery* Apoorva Rajagopal and colleagues, in a collaboration between Stanford University, the University of Minnesota, and Gillette Children's Specialty Healthcare, have used gastrocnemius lengths predicted via an OpenSim model to predict gait changes following gastrocnemius lengthening surgery in children with cerebral palsy. The paper was recently published in *PLOS ONE* and is accompanied by the motion data used in the study and an Excel spreadsheet that allows the calculation of gastrocnemius lengths from clinical gait analysis data. Read more <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0233706> . -- *Jennifer Hicks, Ph.D.* Director of Data Science | Mobilize Center <http://mobilize.stanford.edu> Associate Director | NCSRR <http://www.stanford.edu/group/opensim/about/index.html> R&D Manager | OpenSim <http://opensim.stanford.edu/> Stanford University 650-498-4403 | jenhicks(a)stanford.edu

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Webinar: Which Simulation Pipeline Should I Use and Recap of Latest Workshop
by Joy P. Ku 21 Apr '20

21 Apr '20

Webinar: Which Simulation Pipeline Should I Use? An Overview of Common Workflows April 29, 2020 at 8:00 a.m. Pacific Daylight Saving Time We invite you to join us for a webinar featuring Carmichael Ong from the OpenSim team at Stanford University. In this webinar, Dr. Ong will describe different simulation pipelines used to understand how movement is coordinated: inverse dynamics, static optimization computed muscle control, forward dynamics, shooting methods, reinforcement learning, and direct collocation. He will compare and contrast the pipelines and provide case studies to illustrate how to select a pipeline. Learn more and register<https://stanford.webex.com/stanford/onstage/g.php?MTID=e54fe3901221c30282b7…> Diverse Research and Methods Advanced at Recent Workshop Twenty-three individuals from around the world joined us virtually for our Advanced User Workshop from March 24-26, 2020. During the three-day event, individuals worked closely with the NCSRR staff through Zoom and Slack to advance their projects. Many of the projects utilized the recently released OpenSim Moco<http://opensim.stanford.edu/moco> software, taking advantage of its ability to predict motion and optimize parameters. Examples of Moco-based projects include predicting the dynamics of knee alignment surgery; studying perturbations to standing balance; developing a framework for optimizing ankle sprain prevention; and analyzing shoulder movements after reverse total shoulder arthroplasty. Other projects applied a traditional OpenSim pipeline to their research, for example, to design a hypogravity exercise device or understand chronic ankle instability. And some projects were developing new tools and methods, such as integrating the EZC3D toolbox with OpenSim or creating a pipeline to use tensiometer data to create high-fidelity subject-specific knee models. Learn more about these and other workshop projects<http://ow.ly/rTUG50z8dCH> --- Joy P. Ku, PhD Project Manager, SimTK<http://simtk.org/> Director of Communications & Training, NCSRR<http://opensim.stanford.edu/> Director of Communications & Engagement, Mobilize Center<http://mobilize.stanford.edu/> Stanford University (w) 650.736.8434 Email: joyku(a)stanford.edu<mailto:joyku@stanford.edu>

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Webinar on Characterizing Hyperreflexia and Abnormal Coordination in Post-Stroke Stiff-Knee Gait and More
by Joy P. Ku 28 Feb '20

28 Feb '20

Webinar: Characterizing Hyperreflexia and Abnormal Coordination in Post-Stroke Stiff-Knee Gait March 12, 2020 at 10:00 a.m. Pacific Daylight Time We invite you to join us for a webinar featuring Tunc Akbas from Harvard University. In this webinar, Dr. Akbas will describe an OpenSim-based framework to investigate the neuromuscular mechanisms of abnormal coordination in post-stroke stiff-knee gait. He will discuss their simulation results and also the use of their framework as a template for exoskeletal assistance post-stroke. Learn more and register<https://stanford.webex.com/mw3300/mywebex/default.do?nomenu=true&siteurl=st…> New Release OpenSim 4.1 Supports Inertial Measurement Unit (IMU) Data If you haven't tried out the latest release of OpenSim, we encourage you to download OpenSim 4.1<https://simtk.org/frs/?group_id=91> today. The new software enables users to read in inertial measurement unit (IMU) data and compute inverse kinematics based on IMU orientations. This workflow is called OpenSense. For this release, the user is primarily responsible for ensuring proper calibration and registration of the sensors to an appropriate OpenSim model. Future releases will streamline and enhance this process. This is an exciting initial step towards supporting biomechanical analyses with IMUs in OpenSim. We have also fixed several bugs and improved the user experience. Read more and learn how to upgrade<https://simtk-confluence.stanford.edu/pages/viewpage.action?pageId=36439186> Follow Us on Twitter Our Twitter feed provides additional news that might be of interest to the biomechanics and rehab community. This includes funding opportunities, job postings, and workshop announcements from the NIH and other organizations, in addition to real-time updates on OpenSim events and OpenSim projects from around the world. Follow us on Twitter:<https://twitter.com/OpenSimSU> @OpenSimSU<https://twitter.com/OpenSimSU> --- Joy P. Ku, PhD Project Manager, SimTK<http://simtk.org/> Director of Communications & Training, NCSRR<http://opensim.stanford.edu/> Director of Communications & Engagement, Mobilize Center<http://mobilize.stanford.edu/> Stanford University (w) 650.736.8434 Email: joyku(a)stanford.edu<mailto:joyku@stanford.edu>

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