About#

Overview#

Cleaver is an open-source multi-material tetrahedral meshing tool that creates conforming tetrahedral meshes for multimaterial or multiphase volumetric data. These meshes ensure both geometric accuracy and bounded element quality using the Lattice Cleaving algorithm.

Method#

The Cleaver Library is based on the Lattice Cleaving algorithm.

The method is a stencil-based approach, and relies on an octree structure to provide a coarse level of grading in regions of homogeneity. The cleaving algorithm works by utilizing indicator functions, which indicate the strength or relative presence of a particular material. At each point, only the material with the largest indicator value is considered present.

The method is theoretically guaranteed to produce valid meshes with bounded dihedral angles, while still conforming to multimaterial material sur- faces. Empirically these bounds have been shown to be well within useful ranges, thus creating efficient meshes for analysis, simulation, and visualization.

Reference:

Bronson J., Levine, J., Whitaker R., “Lattice Cleaving: Conforming Tetrahedral Meshes of Multimaterial Domains with Bounded Quality”. Proceedings of the 21st International Meshing Roundtable (San Jose, CA, Oct 7-10, 2012)

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190882/

Authors#

Cleaver is an open-source project with a growing community of contributors. The software was initially developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.

Many Cleaver contributors are listed in the Contributors Graph. However, the following authors have made significant contributions to the conception, design, or implementation of the software and are considered “The Cleaver Developers”:

  • Jonathan Bronson

  • Brig Bagley

  • Jess Tate

  • Ally Warner

  • Dan White

  • Ross Whitaker

Acknowledgement#

This project was supported by the National Institute of General Medical Sciences of the National Institutes of Health under grant numbers P41 GM103545 and R24 GM136986.

Citing Cleaver#

When citing Cleaver in your scientific research, please mention the following work to support increased visibility and dissemination of our software:

Cleaver: A MultiMaterial Tetrahedral Meshing Library and Application. Scientific Computing and Imaging Institute (SCI), Download from: http://www.sci.utah.edu/software.html, 2015.

For your convenience, you may use the following BibTex entry:

@Misc{SCI:Cleaver,
  author =    "CIBC",
  year =      "2015",
  note =      "Cleaver: A MultiMaterial Tetrahedral Meshing
              Library and Application. Scientific Computing and
              Imaging Institute (SCI), Download from:
              http://www.sci.utah.edu/software.html",
  keywords =  "Cleaver, CIBC",
}

Bibliography#

Below is a list of publications that reference Cleaver.

Note

Please note that this list only includes citations from publications published after 2017 and not involving researchers or developers from the SCI Institute.

  1. Frank Abdi, Harsh Baid, Rashid Miraj, Beth Clarkson, and Jacob Fish. Computational approaches for composite materials. In Composite Materials Qualification. Begell House, 2021.

  2. Sahar Bakhshian, Zhuofan Shi, Muhammad Sahimi, Theodore T Tsotsis, and Kristian Jessen. Image-based modeling of gas adsorption and deformation in porous media. Scientific reports, 8(1):1–12, 2018.

  3. Julia Boonzaier, Petar I Petrov, Willem M Otte, Nickolay Smirnov, Sebastiaan FW Neggers, and Rick M Dijkhuizen. Design and evaluation of a rodent-specific transcranial magnetic stimulation coil: an in silico and in vivo validation study. Neuromodulation: Technology at the Neural Interface, 23(3):324–334, 2020.

  4. Mar Cortes, Laura Dubreuil Vall, Giulio Ruffini, Douglas Labar, and Dylan Edwards. Transcranial direct current stimulation in chronic spinal cord injury: quantitative eeg study. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10(1):e13, 2017.

  5. Fotios Drakopoulos. Finite element modeling driven by health care and aerospace applications. PhD thesis, Old Dominion University, 2017.

  6. Jacob Fish and Nan Hu. Multiscale modeling of femur fracture. International Journal for Numerical Methods in Engineering, 111(1):3–25, 2017.

  7. Kathleen M Friel, Peter Lee, Disha Gupta, Hsing-Ching Kuo, Ana RP Smorenburg, and Dylan J Edwards. Combined transcranial direct current stimulation and upper extremity robotic therapy improves upper extremity function in an adult with cerebral palsy: a pilot study. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10(1):e13, 2017.

  8. Eloy García, Yago Diez, Oliver Diaz, Xavier Lladó, Robert Martí, Joan Martí, and Arnau Oliver. A step-by-step review on patient-specific biomechanical finite element models for breast mri to x-ray mammography registration. Medical physics, 45(1):e6–e31, 2018.

  9. Ho Quang Nguyen, Tien Tuan Dao, Alain Rassineux, and Marie Christine Ho Ba Tho. Material-driven mesh of the lumbar spine derived from ct data. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 6(2):128–136, 2018.

  10. Anh Phong Tran and Qianqian Fang. Fast and high-quality tetrahedral mesh generation from neuroanatomical scans. arXiv preprint arXiv:1708.08954, 2017.

  11. Anh Phong Tran, Shijie Yan, and Qianqian Fang. Improving model-based functional near-infrared spectroscopy analysis using mesh-based anatomical and light-transport models. Neurophotonics, 7(1):015008, 2020.

  12. Laura Dubreuil Vall, Mar Cortes, Dylan Edwards, Giulio Ruffini, and David Putrino. Eeg recordings during sham control transcranial direct current stimulation protocol. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation, 10(1):e13, 2017.

  13. Jared Vicory, Ethan Murphy, and Ryan J Halter. Creation and visualization of high-quality tetrahedral meshes from segmentations using 3d slicer. ELECTRICAL IMPEDANCE TOMOGRAPHY, pages 55, 2018.

  14. Charlotte E Vorwald, Shreeya Joshee, and J Kent Leach. Spatial localization of endothelial cells in heterotypic spheroids influences notch signaling. Journal of Molecular Medicine, 98(3):425–435, 2020.

  15. Chuan Wang, Jie Zhu, Yanwen Guo, and Wenping Wang. Video vectorization via tetrahedral remeshing. IEEE Transactions on Image Processing, 26(4):1833–1844, 2017.

  16. Karissa M Wang, Amanda J Rickards, Trevor Bingham, Jonathan D Tward, and Ryan G Price. Evaluation of a silicone-based custom bolus for radiation therapy of a superficial pelvic tumor. Journal of Applied Clinical Medical Physics, pages e13538, 2022.

  17. Jing Xu. Automatic Linear and Curvilinear Mesh Generation Driven by Validity Fidelity and Topological Guarantees. PhD thesis, Old Dominion University, 2020.

  18. Jing Xu and Andrey N Chernikov. Homeomorphic tetrahedralization of multi-material images with quality and fidelity guarantees. Procedia engineering, 203:40–52, 2017.

  19. Jiayi Yao, Xiuju Wu, Daoqin Zhang, Lumin Wang, Li Zhang, Eric X Reynolds, Carlos Hernandez, Kristina I Boström, Yucheng Yao, and others. Elevated endothelial sox2 causes lumen disruption and cerebral arteriovenous malformations. The Journal of clinical investigation, 129(8):3121–3133, 2019.