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Automated Cell Scale Meshes
This package provides scripts, meshes, and models utilized in the manuscript "Automated Generation of Tissue-Specific Three-Dimensional Finite Element Meshes Containing Ellipsoidal Cellular Inclusions". The scripts provide the capacity to build meshes of prismatic tissue volumes with spherical and/or ellipsoidal inclusions of cells surrounded with a pericellular matrix. The tool requires Python (http://www.python.org) and Salome v6.3.1 (http://www.salome-platform.org/) to operate. Multiple example meshes, all described in the manuscript, are also provided.
version 1.0.0
Jul 19, 2013

  

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Jul 19, 2013
28 KB
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Python scripts to built meshes of tissue blocks with arbitrary size, cell organization, and ellipsoidal cell shapes.

Jul 19, 2013
6 MB
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An example mesh illustrating the capabilities of different tissue block meshes including ellipsoidal cellular inclusions.

Jul 19, 2013
19 MB
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A mesh generated from explicit geometry obtained from confocal laser scanning microscopy of a cell-seeded construct.

Jul 19, 2013
157 MB
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Multiple meshes generated for the transitional zone of knee cartilage utilizing statistical cell information from literature.

Jul 19, 2013
41 MB
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Raw simulation results to compare model predictions of tetrahedral meshes (generated using the scripts) against those of hexahedral meshes.

PLEASE CITE THESE PAPERS

Bennetts, C. J., Sibole, S. and Erdemir, A. Automated generation of tissue-specific three-dimensional finite element meshes containing ellipsoidal cellular inclusions, Computer Methods in Biomechanics and Biomedical Engineering, 18, 1293-1304. (2015)


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Autonomous Pipeline
This package contains i) macroscopic finite element representation of the tibiofemoral joint, ii) two different microscopic finite element representations of chondrocyte environment (single cell vs 11 cell), iii) simulation results for the macroscopic model, iv) simulations result of microscopic models post-processed by macro level solution. The study is conducted through an autonoumous multiscale analysis pipeline described in publications referred below.
version 1.0.0
Oct 25, 2012

  

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Oct 25, 2012
152 MB
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Source code
Contains all scripts and files to reproduce the study with instructions on how to do this on a cluster or locally.

PLEASE CITE THESE PAPERS

Sibole, S. C. and Erdemir, A. (2012) Chondrocyte deformations as a function of tibiofemoral joint loading predicted by a generalized high-throughput pipeline of multi-scale simulations, PLoS ONE, 7, e37538. (2012) View


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Biphasic Multiscale Analysis
This package contains materials to explore data passing assumptions to conduct cell scale biphasic simulations from the results of biphasic tissue simulations. Four cases of tissue loading and boundary conditions were implemented in tissue scale models (four combinations of uniform/nonuniform displacement and symmetric/asymmetric permeability). Two cases of data passing assumptions were tested to drive cell scale models (first order and second order data passing).
version 1.0.0
Oct 25, 2012

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Oct 25, 2012
6 MB
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Source code
Contains all scripts and files to reproduce the study with instructions on how to do this on a cluster or locally.

Oct 25, 2012
344 MB
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Source code
Pre-generated FEBio models for every case.

Oct 25, 2012
359 KB
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Data/images/video
CSV files containing chondrocyte metrics for each simulation and Taylor series tensor coefficients for 1st or 2nd order coupling.

PLEASE CITE THESE PAPERS

Sibole, S. C., Maas, S., Halloran, J. P., Weiss, J. A. and Erdemir, A. Evaluation of a post-processing approach for multiscale analysis of biphasic mechanics of chondrocytes, Computer Methods in Biomechanics and Biomedical Engineering, 16, 1112-1126. (2013) View


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Multiscale data set
This package provides a comprehensive specimen-specific multiscale anatomical and mechanical testing data set for the tibiofemoral joint. For macro and micro scale geometry, magnetic resonance images and histology images are provided respectively. Mechanical testing data at the joint level consists of laxity tests and a combined loading scenario. 12 tissue samples (cartilage, ligaments and menisci) were tested in either compression or tension under stress relaxation conditions to characterize the tissue properties. This data can be useful in developing multi-resolution specimen-specific models of the tibiofemoral joint.
version 1.0.0
Mar 20, 2015

  

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Mar 25, 2015
55 MB
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Data/images/video
This folder contains magnetic resonance images for the knee joint. Please see README-MRI.pdf for content description.

Mar 25, 2015
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Data/images/video
This folder contains the joint mechanical testing data. Please see README-JOINT.pdf for content description.

Mar 25, 2015
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This folder contains the histology data.Please see README-HIST.pdf for content description.

Mar 25, 2015
194 MB
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Data/images/video
This folder contains all the tissue mechanical testing data. Please see README-TISSUE.pdf for content description.

PLEASE CITE THESE PAPERS

Chokhandre, S., Colbrunn, R., Bennetts, C. and Erdemir, A. A comprehensive specimen-specific multiscale data set for anatomical and mechanical characterization of the tibiofemoral Joint, PLoS ONE, 10, e013826. (2015) View


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Single vs. Eleven Cell Study
This package provides scripts, meshes, and models utilized in the manuscript "The Potential for Intercellular Mechanical Interaction - Simulations of Single Chondrocyte Versus Anatomically Based Distribution" (currently ahead of print). The scripts provide the capacity to build meshes, run simulations, and process results for models of biphasic, transition zone chondrocyte mechanics for single and anatomically based eleven cell distributions. The tool requires Python (http://www.python.org) and FEBio v1.5.0 (http://febio.org/) to operate.
1.0.0
Aug 17, 2017

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Aug 17, 2017
7 MB
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