Recurring Meeting of the Advisory Board
Date: April 19, 2018
Due to scheduling conflicts, the group meeting with the Advisory Board members were scheduled as two separate meetings. Please refer to Meeting Minutes for more details.
Project Specific Aims
- To provide an open, freely available, and collaborative development, testing, simulation and dissemination platform for in silico exploration of the biomechanics of healthy and diseased knees.
- To develop in silico biomechanical models of healthy and diseased knee joints of different genders and ages, supported by specimen-specific joint and tissue level experimental mechanics.
https://simtk.org/projects/openknee (project website)
https://simtk.org/plugins/moinmoin/openknee/ (project wiki)
Clinical. Jack Andrish, MD; Carl Winalski, MD; Morgan Jones, MD, MPH; Paul Saluan, MD (Cleveland Clinic)
Engineering. Yasin Dhaher, PhD (Northwestern University); Trent Guess, PhD (University of Missouri), Rami Korhonen, PhD (University of Eastern Finland)
- December 22, 2016 - April 18, 2018
Development Team during Progress Period
Cleveland Clinic Core Team. Ahmet Erdemir, Snehal Chokhandre, Benjamin Landis, Erica Neumann, Tammy Owings, Ariel Schwartz
Stanford University. Scott Delp, Joy Ku, Henry Kwong
University of Utah. Ben Ellis,Steve Maas, Jeff Weiss
Community. Jason Halloran, Will Zaylor
See https://simtk.org/project/memberlist.php?group_id=485 for full details on the project team.
Goals of Progress Period
Plans from previous progress report:
Launch cloud computing at SimTk.org (Stanford University)
- Upgrade Open Knee(s) - Generation 1 to reflect meniscal constraints and in situ ligament strains (Cleveland Clinic)
- Continue implementing additional convenience features for simulation of joint mechanics using FEBio (University of Utah)
- Continue tissue mechanics testing of all specimens (Cleveland Clinic)
Continue development and review of modeling & simulation specifications (Cleveland Clinic & Community)
- Continue developing models for all specimens (Cleveland Clinic)
- Submit publications for Open Knee(s) - Generation 2 data sets (Cleveland Clinic)
- Evaluate and finalize tissue mechanical characterization protocols. Perform repeatability analyses to confirm reliability of specimen-specific tissue properties obtained (Cleveland Clinic).
- Complete segmentation and geometry generation for all specimens (Cleveland Clinic).
Please also refer to previous meeting minutes of the Advisory Board at RecurringMeetings/2016-12-22. Please note that, the project activities and timeline has evolved in an agile manner.
Activities of Progress Period
- Cloud computing
Colud computing interface was fully integrated in SimTk.org as part of the project site. A sample femur-acl-tibia model was provided and can be simulated online by users prescribing desired tibiofemoral joint kinematics.
Tissue mechanical testing protocols for cartilage were finalized after several iterations and modifications. Repeatability tests were conducted for all cartilage samples from oks003. Samples were taken from all relevant locations (medial and lateral femoral condyles, medial and lateral tibial plateau, patella and patellar groove). Unconfined compression, confined compression, and tensile tests were conducted. Each test was repeated 3 times. One compression and one tensile sample was taken from each location and same sample was used for both confined and unconfined compression tests. For three types of tests done on samples from each of the six locations, a total of 54 tests were conducted. Some preliminary statistical analyses were done for all test sets. Further analyses are in progress. Details of the tests and analyses can be found at oks003 cartilage testing
- Protocols are being optimized for meniscus, ligament and tendon mechanical testing.
- Modeling and simulation
Segmentation and geometry generation are complete for all specimens. These may need to be modified if needed during development of models and following simulations. The segmented volumes and geometries are currently available in the source code repository. Please refer to the dashboards in the segmentation and geometry progress section in the Roadmap to get a full picture of the ongoing progress Roadmap.
- Python scripts were developed to automatically generate meshes, assemble the meshes, and generate template models from the given set of surfaces. This pipeline is agnostic to the structures that are being modeled and hence can be utilized for any model development that has multiple connected components. Several improvements have been made over the last progress period to this pipeline and some simulation case studies were performed.
- A full template model was meshed and assembled for specimen oks001 and successfully used for simulation a simple distraction (no contact).
- Data analysis
In order to run simulations and evaluate the performance of the models, joint testing data needs to be extracted in a simplified user-friendly form. A python script was developed that can process experimental data (including registration information) to generate model inputs and visualize the experimental tests in image coordinate system. This is implemented both for tibiofemoral and patellofemoral joints and can accommodate left and right knees. Details can be found at: Joint Testing Data Extraction, Revision as of April 18, 2018 or current version
As of April 19, 2018, Open Knee(s) provided 9 packages (14,504 total downloads, 4,970 unique downloads), see Open Knee(s) download page:
- oks001 version g2-s1-v0.2.0.20150825 (405 unique users as of April 19, 2018)
- oks002 version g2-s2-v0.2.0.20150916 (88 unique users as of April 19, 2018)
- oks003 version g2-s3-v0.2.0.20151013 (49 unique users as of April 19, 2018)
- oks004 version g2-s4-v0.2.0.20151029 (42 unique users as of April 19, 2018)
- oks006 version g2-s6-v0.2.0.20150915 (41 unique users as of April 19, 2018)
- oks007 version g2-s7-v0.2.0.20151021 (45 unique users as of April 19, 2018)
- oks008 version g2-s8-v0.2.0.20151021 (50 unique users as of April 19, 2018)
- oks009 version g2-s9-v0.2.0.20151208 (103 unique users as of April 19, 2018)
Open Knee - Generation 1 versions g1-s1-v22.214.171.1241 & g1-s1-v126.96.36.199 (800 unique users as of April 19, 2018):
As of April 19, 2018, Open Knee(s) provided 11 developer, 6 user documentation in release form, see Open Knee(s) documents page.
- With a few exceptions (as requested by a collaborating team), all of the project website; wiki site, e.g. specifications, meeting minutes; data, source code and outputs (segmented volumes, geometries etc) are publicly accessible.
As of April 18, 2018, Open Knee(s) provided 9 packages (14,502 total downloads, 4,970 unique downloads) and Open Knee(s) website received 26008 page hits in the past 180 Days (3066 Unique Visitors) Open Knee(s) project activity
As of April 18, 2018, Open Knee(s) enabled 24 studies by external research teams, see Open Knee(s) publications page.
- Tissue mechanical testing data will be disseminated in its raw from on the Downloads page.
- Community projects
There were no feedback from the community on specifications disseminated through documents for developers in Open Knee(s) documents page. These specifications are still open for feedback through Open Knee(s) public forums and public write discussion pages at the wiki.
- Cobus Muller (University of Stellenbosch, South Africa), along with Swithin Razu and Trent Guess (University of Missouri), has developed a knee model using oks001 data and has been interacting with Ahmet.
- Ahmet provided lectures to promote modeling and simulation biomechanics, which are relevant to Open Knee(s) activities:
Erdemir, A., Democratization of modeling & simulation in biomechanics: our experience with Open Knee(s), October 26, 2017, Kinesiology Colloquium, Department of Kinesiology, Pennsylvania State University, University Park, PA.
- Drafts for manuscripts on anatomical imaging and model assembly are near completion.
- Chokhandre, S., Bennetts, C. J., Donnola, S. B., Flask, Ceylan Colak, C. A., Bonner, T. F., Colbrunn, R. W., Winalski, C., Erdemir, A. Open Knee(s): Magnetic Resonance Imaging Data for Specimen-Specific Anatomical Reconstruction of Knee Models, to be submitted to Scientific Data.
- Landis, B., Erdemir, A. Prototype for Relational Assembly and Templating of Multi-component Finite Element Models of Biological Structures.
- Manuscripts for joint data mechanics will be completed once relevant data extraction processes are finalized.
- Bonner, T. F., Colbrunn, R. W., Chokhandre, S., Bennetts, C. J., Erdemir, A. (in progress) Open Knee(s): comprehensive tibiofemoral joint testing for specimen-specific next generation knee models, to be submitted to Scientific Data.
- Colbrunn, R. W., Halloran, J., Bonner, T. F., Chokhandre, S., Bennetts, C. J., Erdemir, A. (in progress) Open Knee(s): comprehensive patellofemoral joint testing for specimen-specific next generation knee models, to be submitted to Scientific Data.
- Manuscript detailing the cartilage mechanical testing and repeatability analysis is also being worked on.
- Open Knee(s) team had publications in peer-reviewed journals related to synergistic activities:
Erdemir, A., Hunter, P. J., Holzapfel, G. A., Loew, L. M., Middleton, J., Jacobs, C. R., Nithiarasu, P., Lohner, R., Wei, G., Winkelstein, B. A., Barocas, V. H., Guilak, F., Ku, J., Hicks, J. L., Delp, S., Sacks, M., Weiss, J. A., Ateshian, D. G. A., Maas, S. A., McCulloch, A. D. and Peng, G. C. Y. (in press) Perspectives on sharing models and related resources in computational biomechanics research, Journal of Biomechanical Engineering.
- Open Knee(s) team had related conference abstracts:
- Landis, B. and Erdemir, A. Automation of volumetric mesh generation, mesh assembly and model input from surface representations of tissue structures, 41st Annual Meeting of the American Society of Biomechanics, August 8-11, 2017, Boulder, CO.
- Malik, R. and Erdemir, A. Automated optical thickness measurement system, 2017 Summer Biomechanics, Bioengineering, and Biotransport Conference, June 21-24, 2017, Tucson, AZ.
- Erdemir, A., Bonner, T., Chokhandre, S., Colbrunn, R., Landis, B., Morrill, E., Owings, T. and Schimmoeller, T. Logistics of building virtual specimens for in silico biomechanics, 2017 Biomedical Engineering Society / Food and Drug Administration Frontiers in Medical Devices Conference: Innovations in Modeling and Simulation, May 16-18, 2017, Washington, DC.
Erdemir, A. Democratization of modeling & simulation in biomechanics, 10th Anniversary Multiscale Modeling Consortium Meeting, March 22-24, 2017, Bethesda, MD.
- An abstract was submitted to American Society of Biomechanics annual conference detailing the cartilage mechanical testing work (awaiting response).
- Drafts for manuscripts on anatomical imaging and model assembly are near completion.
Ahmet and Jason Halloran (Cleveland State University), along with Kevin Shelburne and Peter Laz (University of Denver), Carl Imhauser (Hospital for Special Surgery), and Thor Besier (Auckland Bioengineering Institute), received a grant for collaborative work in reproducibility in modeling & simulation of the knee joint. Knee Hub
- Open Knee(s) attended the Frontiers in Medical Devices conference in 2017.
Plans for Next Progress Period (April 20,2018 - May 2019)
- Finalize testing specifications for other tissues and complete repeatability tests for oks003 and potentially extend it to at least one more specimen (Cleveland Clinic)
- Disseminate the tissue testing data for oks003 (Cleveland Clinic)
- Submit publications (Cleveland CLinic)
- Continue model development (Cleveland Clinic)
- Improve the cloud computing platform (Cleveland Clinic, Stanford University)
Launch a searchable data management site on SimTk.org to support organization and dissemination of all Open Knee(s) data. (Cleveland Clinic, Stanford University)
Date, Time, Means:
- April 19, 2018, 9:00 AM EST, Skype (AE,RK)
- April 19, 2018, 1.00 PM EST, Skype (AE,SC,TG,YD,JA,MJ)
- Ahmet Erdemir (Cleveland Clinic)
- Snehal Chokhandre (Cleveland Clinic)
- Jack Andrish (Cleveland Clinic)
- Yasin Dhaher (Northwestern University)
- Trent Guess (University of Missouri)
- Morgan Jones (Cleveland Clinic)
- Rami Korhonen (University of Eastern Finland)
- Progress update, see progress report at:
- Recap of previous meeting minutes, see meeting minutes at:
- Action items for following meeting.
Ongoing Action Items:
See notes for details.
- Continue tissue mechanics testing of Open Knee(s) specimens.
- Continue development of Open Knee(s) models.
- Review and submit publications on Open Knee(s) data.
- Snehal summarized where we were as of the last meeting and what has been done since then.
- The emphasis of the updates was mainly on tissue testing and segmentation as these were time consuming and mostly had to be done manually.
- The Cleveland Clinic team aggressively tackled tissue testing in this progress period. After several iterations, a set of protocols was created for cartilage characterization that produced repeatable results.
- Snehal completed repeatability study for oks003 where she tested samples from 6 target locations under confined and unconfined compression as well as tension. Each of these tests was repeated 3 times for a total of 54 tests. This was a very time consuming and extensive process and as per our knowledge the first of its kind of a repeatability data set. The protocols were developed such that the loading rates etc were within physiological limits and also within the capabilities of the testing system.
- The results of these tests appear promising after a preliminary analysis. Further analysis and a manuscript are in the works.
- Trent asked whether this will be extended to other tissues. The Cleveland Clinic team confirmed that the next stage of tissue testing will be to develop specifications for menisci, ligaments and tendons and at the least complete the set for oks003.
- Ahmet also commented that the importance of such a data set is not just characterization of the tissue properties but also the fact that it allows to capture the experimental uncertainties.
- The Cleveland Clinic team has also been working on segmentation of the imaging data to build specimen-specific geometries for finite element models.
- Segmentation has been a bottleneck mainly because most of it has to be done manually and Snehal was mainly the only person working on them.
- All the segmentations are complete as of today (may need some development). Details of all are uploaded on the Roadmap wiki page.
- Ahmet raised the possibility to reach out to the advisory board for quality assurance of segmentations; in particular ligaments.
- Trent asked how others are doing segmentation and whether statistical shape modeling or other automated methods may be useful. Snehal commented that it mostly has to do with the quality of the images and our MRI data was acquired on a 3T magnet with specific protocols for various tissues but still mostly manual intervention was necessary. Also even with automated/ semi-automated systems some form of manual quality check will be required.
- Ahmet commented that both tissue testing and segmentation are manual grueling work and most of the year was spent on getting that done so other components can be work on which we will be able to automate (and have been to some extent).
- Ahmet commented that we have hired new engineers (Ben, Rici, Tyler) to work on another grant but they have been very helpful in building tools that can be used by Open Knees.
- A pipeline was built by Ben to automate mesh generation and template model assembly which will save the team a lot of time. This pipeline is also agnostic to the geometries meaning that it only requires stl files and does not matter what those stl files are for (joint, multi layered structures etc)
- Rici wrote scripts to extract joint testing data which will be very useful as the joint data files are not human readable and difficult to navigate.
- Ahmet summarized the modeling workflow for Jack and Morgan and emphasized how automating these processes will save us a lot of time and help us get repeatable outputs which is challenging if node sets etc have to be picked manually.
Ahmet summarized the KneeHub grant; five different groups build knee models from the same data; compare outputs at different stages to see if different approaches lead to same results.
- Cleveland Clinic team is also working on submitting a manuscript to Scientific Data summarizing the MRI data.
- Morgan asked about validating the models and commented that if done this dataset many be useful to replace cadaver studies with virtual knees.
- Snehal also mentioned that all the tissue samples are preserved and may be imaged or tested again, if needed. In the future, it may also be useful to get a more extensive regional map of tissue properties as there is a significant variation in properties within the same specimen.
- Ahmet apologized for not organizing an update meeting earlier.
- Yasin mentioned that he has several modeling ideas and will be interested in discussing them in the future.