A set of FEniCS- and VTK-based python tools for Finite Element Digital Image Correlation/Image Registration/Motion Tracking, basically implementing the method described in [[Genet, Stoeck, von Deuster, Lee & Kozerke (2018). Equilibrated Warping: Finite Element Image Registration with Finite Strain Equilibrium Gap Regularization. Medical Image Analysis, 50, 1–22.]](https://doi.org/10.1016/j.media.2018.07.007) and [[Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique, 351, 429-458.]](https://doi.org/10.5802/crmeca.228).
A set of FEniCS- and VTK-based python tools for Finite Element Digital Image Correlation/Image Registration/Motion Tracking, basically implementing the method described in [[Genet, Stoeck, von Deuster, Lee & Kozerke (2018). Equilibrated Warping: Finite Element Image Registration with Finite Strain Equilibrium Gap Regularization. Medical Image Analysis, 50, 1–22.](https://doi.org/10.1016/j.media.2018.07.007)] and [[Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique, 351, 429-458.](https://doi.org/10.5802/crmeca.228)].
The library has notably been used in:
*[[Zou, Xi, Zhao, Koh, Gao, Su, Tan, Allen, Lee, Genet & Zhong (2018). Quantification of Biventricular Strains in Heart Failure With Preserved Ejection Fraction Patient Using Hyperelastic Warping Method. Frontiers in Physiology.]](https://doi.org/10.3389/fphys.2018.01295)
*[[Finsberg, Xi, Tan, Zhong, Genet, Sundnes, Lee & Wall (2018). Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization. International Journal for Numerical Methods in Biomedical Engineering.]](https://doi.org/10.1002/cnm.2982)
*[[Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2019). Validation of Finite Element Image Registration‐based Cardiac Strain Estimation from Magnetic Resonance Images. PAMM.]](https://doi.org/10.1002/pamm.201900418)
*[[Finsberg, Xi, Zhao, Tan, Genet, Sundnes, Lee, Zhong & Wall (2019). Computational quantification of patient-specific changes in ventricular dynamics associated with pulmonary hypertension. American Journal of Physiology-Heart and Circulatory Physiology.]](https://doi.org/10.1152/ajpheart.00094.2019)
*[[Lee & Genet (2019). Validation of Equilibrated Warping—Image Registration with Mechanical Regularization—On 3D Ultrasound Images. Functional Imaging and Modeling of the Heart (FIMH). Cham: Springer International Publishing.]](https://doi.org/10.1007/978-3-030-21949-9_36)
*[[Škardová, Rambausek, Chabiniok & Genet (2019). Mechanical and Imaging Models-Based Image Registration. VipIMAGE 2019. Cham: Springer International Publishing.]](https://doi.org/10.1007/978-3-030-32040-9_9)
*[[Zou, Leng, Xi, Zhao, Koh, Gao, Tan, Tan, Allen, Lee, Genet & Zhong (2020). Three-dimensional biventricular strains in pulmonary arterial hypertension patients using hyperelastic warping. Computer Methods and Programs in Biomedicine.]](https://doi.org/10.1016/j.cmpb.2020.105345)
*[[Gusseva, Hussain, Friesen, Moireau, Tandon, Patte, Genet, Hasbani, Greil, Chapelle & Chabiniok (2021). Biomechanical Modeling to Inform Pulmonary Valve Replacement in Tetralogy of Fallot Patients after Complete Repair. Canadian Journal of Cardiology.]](https://doi.org/10.1016/j.cjca.2021.06.018)
*[[Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2021). In-silico study of accuracy and precision of left-ventricular strain quantification from 3D tagged MRI. PLOS ONE.]](https://doi.org/10.1371/journal.pone.0258965)
*[[Castellanos, Škardová, Bhattaru, Berberoğlu, Greil, Tandon, Dillenbeck, Burkhardt, Hussain, Genet & Chabiniok (2021). Left Ventricular Torsion Obtained Using Equilibrated Warping in Patients with Repaired Tetralogy of Fallot. Pediatric Cardiology.]](https://doi.org/10.1007/s00246-021-02608-y)
*[[Berberoğlu, Stoeck, Kozerke & Genet (2022). Quantification of left ventricular strain and torsion by joint analysis of 3D tagging and cine MR images. Medical Image Analysis.]](https://doi.org/10.1016/j.media.2022.102598)
*[[Patte, Brillet, Fetita, Gille, Bernaudin, Nunes, Chapelle & Genet (2022). Estimation of regional pulmonary compliance in idiopathic pulmonary fibrosis based on personalized lung poromechanical modeling. Journal of Biomechanical Engineering.]](https://doi.org/10.1115/1.4054106)
*[[Laville, Fetita, Gille, Brillet, Nunes, Bernaudin & Genet (2023). Comparison of optimization parametrizations for regional lung compliance estimation using personalized pulmonary poromechanical modeling. Biomechanics and Modeling in Mechanobiology.]](https://doi.org/10.1007/s10237-023-01691-9)
*[[Genet, Stoeck, von Deuster, Lee & Kozerke (2018). Equilibrated Warping: Finite Element Image Registration with Finite Strain Equilibrium Gap Regularization. Medical Image Analysis, 50, 1–22.](https://doi.org/10.1016/j.media.2018.07.007)]
*[[Zou, Xi, Zhao, Koh, Gao, Su, Tan, Allen, Lee, Genet & Zhong (2018). Quantification of Biventricular Strains in Heart Failure With Preserved Ejection Fraction Patient Using Hyperelastic Warping Method. Frontiers in Physiology.](https://doi.org/10.3389/fphys.2018.01295)]
*[[Finsberg, Xi, Tan, Zhong, Genet, Sundnes, Lee & Wall (2018). Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization. International Journal for Numerical Methods in Biomedical Engineering.](https://doi.org/10.1002/cnm.2982)]
*[[Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2019). Validation of Finite Element Image Registration‐based Cardiac Strain Estimation from Magnetic Resonance Images. PAMM.](https://doi.org/10.1002/pamm.201900418)]
*[[Finsberg, Xi, Zhao, Tan, Genet, Sundnes, Lee, Zhong & Wall (2019). Computational quantification of patient-specific changes in ventricular dynamics associated with pulmonary hypertension. American Journal of Physiology-Heart and Circulatory Physiology.](https://doi.org/10.1152/ajpheart.00094.2019)]
*[[Lee & Genet (2019). Validation of Equilibrated Warping—Image Registration with Mechanical Regularization—On 3D Ultrasound Images. Functional Imaging and Modeling of the Heart (FIMH). Cham: Springer International Publishing.](https://doi.org/10.1007/978-3-030-21949-9_36)]
*[[Škardová, Rambausek, Chabiniok & Genet (2019). Mechanical and Imaging Models-Based Image Registration. VipIMAGE 2019. Cham: Springer International Publishing.](https://doi.org/10.1007/978-3-030-32040-9_9)]
*[[Zou, Leng, Xi, Zhao, Koh, Gao, Tan, Tan, Allen, Lee, Genet & Zhong (2020). Three-dimensional biventricular strains in pulmonary arterial hypertension patients using hyperelastic warping. Computer Methods and Programs in Biomedicine.](https://doi.org/10.1016/j.cmpb.2020.105345)]
*[[Gusseva, Hussain, Friesen, Moireau, Tandon, Patte, Genet, Hasbani, Greil, Chapelle & Chabiniok (2021). Biomechanical Modeling to Inform Pulmonary Valve Replacement in Tetralogy of Fallot Patients after Complete Repair. Canadian Journal of Cardiology.](https://doi.org/10.1016/j.cjca.2021.06.018)]
*[[Berberoğlu, Stoeck, Moireau, Kozerke & Genet (2021). In-silico study of accuracy and precision of left-ventricular strain quantification from 3D tagged MRI. PLOS ONE.](https://doi.org/10.1371/journal.pone.0258965)]
*[[Castellanos, Škardová, Bhattaru, Berberoğlu, Greil, Tandon, Dillenbeck, Burkhardt, Hussain, Genet & Chabiniok (2021). Left Ventricular Torsion Obtained Using Equilibrated Warping in Patients with Repaired Tetralogy of Fallot. Pediatric Cardiology.](https://doi.org/10.1007/s00246-021-02608-y)]
*[[Berberoğlu, Stoeck, Kozerke & Genet (2022). Quantification of left ventricular strain and torsion by joint analysis of 3D tagging and cine MR images. Medical Image Analysis.](https://doi.org/10.1016/j.media.2022.102598)]
*[[Patte, Brillet, Fetita, Gille, Bernaudin, Nunes, Chapelle & Genet (2022). Estimation of regional pulmonary compliance in idiopathic pulmonary fibrosis based on personalized lung poromechanical modeling. Journal of Biomechanical Engineering.](https://doi.org/10.1115/1.4054106)]
*[[Laville, Fetita, Gille, Brillet, Nunes, Bernaudin & Genet (2023). Comparison of optimization parametrizations for regional lung compliance estimation using personalized pulmonary poromechanical modeling. Biomechanics and Modeling in Mechanobiology.](https://doi.org/10.1007/s10237-023-01691-9)]
*[[Genet (2023). Finite strain formulation of the discrete equilibrium gap principle: application to mechanically consistent regularization for large motion tracking. Comptes Rendus Mécanique, 351, 429-458.](https://doi.org/10.5802/crmeca.228)]
(If you use it for your own work please let me know!)
### Tutorials
Interactive tutorials can be found at https://mgenet.gitlabpages.inria.fr/dolfin_warp-tutorials/index.html.
Interactive tutorials can be found at [https://mgenet.gitlabpages.inria.fr/dolfin_warp-tutorials](https://mgenet.gitlabpages.inria.fr/dolfin_warp-tutorials).
