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 * Complete all segmentation and geometry generation for all specimens (Cleveland Clinic).
 * Continue development for specifications for model development(Cleveland Clinic).
 * Complete segmentation and geometry generation for all specimens (Cleveland Clinic).
 * Continue development of specifications for model development (Cleveland Clinic).
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 * Submit publications for Open Knee(s)(Cleveland Clinic).  * Submit publications for Open Knee(s) (Cleveland Clinic).

Please also refer to previous meeting minutes of the Advisory Board at RecurringMeetings/2016-12-22
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 * Tissue mechanical testing
 * Segmentation and geometry generation
 * Meshing and model assembly using previously developed pipeline
 * Experimentation
   * Tissue mechanical testing protocols for cartilage were finalized after several iterations and modifications. Repeatability tests were conducted for cartilage samples from oks003. Samples were taken from all relevant locations (Medial laetral 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 basic statistical analyses were done for all test sets. Further analyses are in progress. Details of the tests and analyses can be found at [[https://simtk.org/svn/openknee/doc/tissue_mechanical_testing/oks003-cartilage-repeatability-analysis.pdf| oks003 cartilage testing]]
  * Protocols are being optimized for meniscus, ligament and tendon mechanical testing.

 * Modeling and simulation
  * Segmentation and geometries generation is complete for all specimens. They may be modified/ fixed if needed for developing and running the models. The segmented volumes and geometries are 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 progress made[[roadmap link]].
  * Python scripts were developed in the previous year to automatically generate meshes, assemble the meshes and generate 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 were made over the last progress period in this pipeline and some simulation case studies were performed.
  * A full model was meshed and assembled for oks001 and successfully ran under simple uniaxial extension (distraction).
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 * Modeling and simulation
 * MRI data manuscript submission
 * Cartilage mechanical testing manuscript, TF joint and PF joint manuscripts.
 * Data management site development.
 * Dissemination – tissue mechanical testing data, segmentation and geometries
  * In order to run and validate the models, joint testing data needs to be extracted in simplified user readable form. A python script was developed that can extract experimental data for model inputs and visualize the experiemntal tests in image coordinate system. This is implemented for both tibiofemoral and patellofemoral joints and can accommodate both left and right knees. Details can be found at: [[https://simtk.org/plugins/moinmoin/openknee/Specifications/ModelingKinematicsKinetics/Discussion| Joint data extraction]]

 * Publications
  * 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 (will be submitted to Scientific Data (Nature)).
 * Ben Landis, Ahmet 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 in place.
          * 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.

 * Dissemination
  * Tissue mechanical testing data will be disseminated in its raw from on downloads 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)
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 * Other – (conferences, KneeHub)   * There were no feedbacks 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.
  * Ahmet Erdemir provided lectures to promote modeling and simulation biomechanics, which are relevant to Open Knee(s) activities:
     * Democratization of modeling and simulation in biomechanics: Our experience with Open Knee(s). Kinesiology Colloquium Seminar. Pennsylvania State University. 2017.


 * Other
  * 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 link]]
 * DC conference
 * ASB 2018
 * MSM 2018
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 * Complete repeatability tests for oks003 and extend it to at least one more specimen.  * finalize testing specifications for other tissues and Complete repeatability tests for oks003 and extend it to at least one more specimen.
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 * Data management site?  * Data management site launch

Recurring Meeting of the Advisory Board

Date: April 19, 2018


Progress Report

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.

Project Infrastructure

Project Contact

Advisory Board

  • 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)

Progress Period

December 22, 2016 - April 18, 2018.

Development Team during Progress Period

  • Cleveland Clinic Core Team. Snehal Chokhandre, Ahmet Erdemir, Ben Landis, Rici Nuemann, Tammy Owings, Ariel Schwartz.

  • Stanford University. Scott Delp, Joy Ku, Henry Kwong

  • University of Utah. Ben Ellis,Steve Maas, Jeff Weiss

  • Community. Jason Halloran, Connor Lough, Raghav Malik, Will Zaylor

See https://simtk.org/project/memberlist.php?group_id=485 for full details on the project team.

Goals of Progress Period

  • 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).
  • Continue development of specifications for model development (Cleveland Clinic).
  • Continue developing models for all specimens(Cleveland Clinic).
  • Submit publications for Open Knee(s) (Cleveland Clinic).

Please also refer to previous meeting minutes of the Advisory Board at RecurringMeetings/2016-12-22

Activities of Progress Period

  • Experimentation
    • Tissue mechanical testing protocols for cartilage were finalized after several iterations and modifications. Repeatability tests were conducted for cartilage samples from oks003. Samples were taken from all relevant locations (Medial laetral 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 basic 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 geometries generation is complete for all specimens. They may be modified/ fixed if needed for developing and running the models. The segmented volumes and geometries are 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 progress maderoadmap link.

    • Python scripts were developed in the previous year to automatically generate meshes, assemble the meshes and generate 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 were made over the last progress period in this pipeline and some simulation case studies were performed.
    • A full model was meshed and assembled for oks001 and successfully ran under simple uniaxial extension (distraction).
  • Joint testing data extraction
    • In order to run and validate the models, joint testing data needs to be extracted in simplified user readable form. A python script was developed that can extract experimental data for model inputs and visualize the experiemntal tests in image coordinate system. This is implemented for both tibiofemoral and patellofemoral joints and can accommodate both left and right knees. Details can be found at: Joint data extraction

  • Publications
    • 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 (will be submitted to Scientific Data (Nature)).
      • Ben Landis, Ahmet 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 in place.
      • 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.
  • Dissemination
    • Tissue mechanical testing data will be disseminated in its raw from on downloads 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)
  • Community projects
    • There were no feedbacks 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.
    • Ahmet Erdemir provided lectures to promote modeling and simulation biomechanics, which are relevant to Open Knee(s) activities:
      • Democratization of modeling and simulation in biomechanics: Our experience with Open Knee(s). Kinesiology Colloquium Seminar. Pennsylvania State University. 2017.
  • Other
    • 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 link

  • DC conference
  • ASB 2018
  • MSM 2018

Plans for Next Progress Period (April 20,2018 - May 2019)

  • finalize testing specifications for other tissues and Complete repeatability tests for oks003 and extend it to at least one more specimen.
  • Submit further publications
  • Continue model development
  • Cloud computing?
  • Data management site launch
  • Submit supporting grant applications

Meeting Minutes

Date, Time, Means:

Attendees:

Agenda:

Ongoing Action Items:

See notes for details.

Notes:

RecurringMeetings/2018-04-19 (last edited 2018-06-07 15:16:37 by snehalkc)