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* Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * builds with pip adds pyproject.toml build command: pip install --no-build-isolation --config-settings=editable.rebuild=true -ve. * debugging, still no build apparently * build and tests * update nb submodule * fix pyproject * install with pip in CI * install with pip in CI * install with pip in CI * adds scikit-build dep * python version * python version specifier * remove strang flags * adds _version.py * setuptools_scm dep * simplified I guess * zdds setuptools-scm to env, MakeFilelist shenanigans * restricting to 3.10 * install dev * pyhon version coherence * install cmd * trying to move to modern sckit-build (it's painful) * WIP change build * getting closer I hope * make_spherical test pasess \o/ * tests passing, warnings still to be treated * don't install editable version in gh action * remove diff chars * tagging again to avoid metadata mismatch * Uncomment 2D repulsion + tests Fix pandas issue * Add comments in effectors.py * rmeove _version.py and ignore in git * Update history.py (#274) > Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded. * skip 2 tests * fix non existing hdf5 * submodules * adds notebooks submodule * should fix history bug * adds submodules again --------- Co-authored-by: Sophie T <[email protected]> Co-authored-by: sniffo <[email protected]>
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| ## pytest | ||
| .pytest_cacheflycheck_* | ||
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| .idea/ | ||
| src/tyssue/_version.py | ||
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| url = https://[email protected]/pybind/pybind11.git | ||
| [submodule "doc/notebooks"] | ||
| path = doc/notebooks | ||
| url = https://github.com/DamCB/tyssue-demo | ||
| url = git@github.com:damcb/tyssue-demo.git | ||
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@@ -28,41 +28,45 @@ This commit to the **new default branch `main` is the official start of the 1.0 | |
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| <hr/> | ||
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| [](http://tyssue.readthedocs.io/en/latest/ | ||
| ) | ||
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| [](https://zenodo.org/badge/latestdoi/32533164) [](https://gitter.im/DamCB/tyssue?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) | ||
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| | Name | Downloads | Version | Platforms | | ||
| | --- | --- | --- | --- | | ||
| | [](https://anaconda.org/conda-forge/tyssue) | [](https://anaconda.org/conda-forge/tyssue) | [](https://anaconda.org/conda-forge/tyssue) | [](https://anaconda.org/conda-forge/tyssue) | | ||
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| # tyssue is now published in the Journal of Open Source Software! | ||
| | Coverage | Doc | CHAT | | ||
| | --- | --- | --- | | ||
| | [](https://coveralls.io/r/DamCB/tyssue) | [](http://tyssue.readthedocs.io/en/latest/) | [](https://gitter.im/DamCB/tyssue?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) | | ||
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| [](https://doi.org/10.21105/joss.02973) | ||
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| # tyssue is now published in the Journal of Open Source Software! | ||
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| | ZENODO DOI | JOSS DOI | | ||
| | --- | --- | | ||
| | [](https://zenodo.org/badge/latestdoi/32533164) | [](https://doi.org/10.21105/joss.02973) | | ||
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| The `tyssue` library seeks to provide a unified interface to implement | ||
| bio-mechanical models of living tissues. | ||
| biomechanical models of living tissues. | ||
| It's main focus is on **vertex based epithelium models**. | ||
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| ## Overview | ||
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| ### What kind of Models does it implement? | ||
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| The first model implemented is the one described in | ||
| Monier et al. [monier2015apico]. It is an example of a vertex model, | ||
| Monier et al.<sup id="a1">[1](#f1)</sup>. It is an example of a vertex model, | ||
| where the interactions are only evaluated on the apical surface sheet | ||
| of the epithelium. The second class of models is still at an | ||
| of the epithelium. The second class of models is still at a | ||
| stage. They implement a description of the tissue's rheology, within a | ||
| dissipation function formalism. | ||
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|  | ||
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| ### What kind of geometry does it model ? | ||
| `tyssue` allows to model different geometries in 2D and in 3D. Presentation of the different geometries and how to create them are shown in this [notebook](https://github.com/DamCB/tyssue-demo/blob/master/01-Geometry.ipynb). | ||
| <p align="center"> | ||
| <img src="doc/illus/geometry.png" width="500"> | ||
| </p> | ||
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| ### General Structure of the modeling API | ||
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| #### Design principles | ||
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| Each biological question, be it in morphogenesis or cancer studies is | ||
| unique, and requires tweeking of the models developed by the | ||
| physicists. Most of the modelling softwares follow an architecture | ||
| physicists. Most of the modelling software follow an architecture | ||
| based on a core C++ engine with a combinaison of markup or scripting | ||
| capacities to run specific simulation. | ||
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| > Separate structure, geometry and models | ||
| We seek to have a design as modular as possible, to allow the same | ||
| epithlium mesh to be fed to different physical models. | ||
| epithelium mesh to be fed to different physical models. | ||
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| > Accessible, easy to use data structures | ||
| The core of the tyssue library rests on two structures: a set of | ||
| `pandas DataFrame` holding the tissue geometry and associated data, | ||
| and nested dictionnaries holding the model parameters, variables and | ||
| and nested dictionaries holding the model parameters, variables and | ||
| default values. | ||
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|  | ||
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| The mesh structure is heavily inspired by | ||
| [CGAL Linear Cell Complexes](http://doc.cgal.org/latest/Linear_cell_complex/index.html), | ||
| most importantly, in the case of a 2D vertex sheet for example, each | ||
| junction edge between the cells is "splitted" between two oriented **half | ||
| junction edge between the cells is "splited" between two oriented **half | ||
| edges**. | ||
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| fig, ax = sheet_view(sheet) | ||
| ``` | ||
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| ### Features | ||
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| * Easy data manipulation. | ||
| * Multiple geometries (Sheets in 2D and 3D, monolayers, bulk). | ||
| * Easy to extend. | ||
| * 2D (matplotlib) and 3D (ipyvolume) customisable visualisation. | ||
| * Easy quasistatic model definition. | ||
| * Self collision detection. **new in 0.3** | ||
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| ### Documentation | ||
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| * The documentation is now browsable on [tyssue.io](http://tyssue.io) | ||
| * The old documentation is still browsable online [here](http://tyssue.readthedocs.io/en/latest/) | ||
| * Introduction notebooks are available [here](https://github.com/DamCB/tyssue-demo). | ||
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| ## Visualisation | ||
| Thanks to @kephale, there is a napari plugin to visualise tyssue simulation output. | ||
| You can find it [here](https://github.com/kephale/napari-tyssue). | ||
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| ### What's new in 1.0 ? | ||
| * No collision in 2D (use effector `Repulsion`) | ||
| * Add new geometry : 2D lateral geometry | ||
| * Add mean calculation in `Epithelium` | ||
| * Add `sheet` conversion to `mesh` from `Meshio` | ||
| * Allow hole in 2D sheet | ||
| * Fix some visualisation | ||
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| ### Roadmap | ||
| You are welcome to participate in the development of `Tyssue`. | ||
| What is planned for the future of `Tyssue`? | ||
| * Solve collision in 2.5D & 3D | ||
| * Use ZARR instead of HDF5 as base file format | ||
| * Upgrade geometry creation | ||
| * Compound geometry to form complex shape | ||
| * Use biological image as blueprint | ||
| * Add rheology model | ||
| * Switch to github-action for continuous integration | ||
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| ### Mailing list: | ||
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| [email protected] - https://framalistes.org/sympa/info/tyssue | ||
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| As all the dependencies are already completely supported in | ||
| python 3.x, **we won't be maintaining a python 2.x version**, because | ||
| it's time to move on... | ||
| <details> | ||
| <summary>Show dependencies</summary> | ||
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| ### Core | ||
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| - coverage | ||
| - pytest-cov | ||
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| </details> | ||
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| ## Install | ||
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| You can install the library with the conda package manager | ||
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| See [INSTALL.md](INSTALL.md) for a step by step install, including the necessary python environment. | ||
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| ## How to cite | ||
| If you find `tyssue` useful please cite [this repository](https://github.com/DamCB/tyssue) using its DOI as follows: | ||
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| ## Licence | ||
| > Theis, Suzanne, Gay, (2021). Tyssue: an epithelium simulation library. Journal of Open Source Software, 6(62), 2973 doi:[https://doi.org/10.21105/joss.02973](https://doi.org/10.21105/joss.02973) | ||
| > | ||
| > Zenodo doi:10.5281/zenodo.4817609 | ||
| Since version 0.3, this project is distributed under the terms of the [General Public Licence](https://www.gnu.org/licenses/gpl.html). | ||
| ## Publications | ||
| If `tyssue` has made a substantial contribution to your work, please edit this file and open a PR. | ||
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| Lou Y, Rupprecht JF, Theis S, Hiraiwa T, and Saunders TE. Curvature-induced cell rearrangements in biological tissues. Phys. Rev. Lett. 2023. doi: [10.1103/PhysRevLett.130.108401](https://doi.org/10.1103/PhysRevLett.130.108401) | ||
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| Versions 2.4 and earlier were distributed under the [Mozilla Public Licence](https://www.mozilla.org/en-US/MPL/2.0/). | ||
| Rahman T, Peters F and Wan LQ. Cell Jamming Regulates Epithelial Chiral Morphogenesis. J Biomech. 2023. doi: [10.1016/j.jbiomech.2023.111435](https://doi.org/10.1016/j.jbiomech.2023.111435) | ||
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| If GPL licencing is too restrictive for your intended usage, please contact the maintainer. | ||
| Fiorentino J and Scialdone A. The role of cell geometry and cell-cell communication in gradient sensing. PLoS Comput Biol. 2022 doi: [10.1371/journal.pcbi.1009552](10.1371/journal.pcbi.1009552) | ||
| Related repository: [https://github.com/ScialdoneLab/2DLEGI](https://github.com/ScialdoneLab/2DLEGI) | ||
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| Courcoubetis G, Xu C, Nuzhdin SV, Haas S. Avalanches during epithelial tissue growth; Uniform Growth and a drosophila eye disc model, PLoS Comput Biol 2022 doi: [10.1371/journal.pcbi.1009952](https://doi.org/10.1371/journal.pcbi.1009952) | ||
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| Martin E, Theis S, Gay G, Monier B, Rouvière C, Suzanne M. Arp2/3-dependent mechanical control of morphogenetic robustness in an inherently challenging environment. Dev Cell. 2021 doi: [10.1016/j.devcel.2021.01.005](https://doi.org/10.1016/j.devcel.2021.01.005) | ||
| Related repository: [https://github.com/suzannelab/polarity](https://github.com/suzannelab/polarity) | ||
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| ## Bibliography | ||
| Gracia M, Theis S, Proag A, Gay G, Benassayag C, Suzanne M. Mechanical impact of epithelial-mesenchymal transition on epithelial morphogenesis in Drosophila. Nat Commun. 2019 doi: [10.1038/s41467-019-10720-0](https://doi.org/10.1038/s41467-019-10720-0) | ||
| Related repository: [https://github.com/suzannelab/invagination](https://github.com/suzannelab/invagination) | ||
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| * There is a [Bibtex file here](doc/bibliography/tyssue.bib) with collected relevant publications. | ||
| Monier B, Gettings M, Gay G, Mangeat T, Schott S, Guarner A, Suzanne M. Apico-basal forces exerted by apoptotic cells drive epithelium folding. Nature. 2015 doi: [10.1038/nature14152](https://doi.org/10.1038/nature14152) | ||
| Related repository: [https://github.com/glyg/leg-joint](https://github.com/glyg/leg-joint) | ||
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| The tyssue library stemed from a refactoring of the `leg-joint` code used in [monier2015apico]. | ||
| ## Licence | ||
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| Since version 0.3, this project is distributed under the terms of the [General Public Licence](https://www.gnu.org/licenses/gpl.html). | ||
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| [monier2015apico]: Monier, B. et al. Apico-basal forces exerted by | ||
| apoptotic cells drive epithelium folding. Nature 518, 245–248 (2015). | ||
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| [Tamulonis2013]: Tamulonis, C. Cell-based models. (Universiteit ven Amsterdam, 2013). doi:10.1177/1745691612459060. | ||
| Versions 2.4 and earlier were distributed under the [Mozilla Public Licence](https://www.mozilla.org/en-US/MPL/2.0/). | ||
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| [Tlili2013]: Tlili,S. et al. Mechanical formalism for tissue dynamics. 6, 23 (2013). | ||
| If GPL licencing is too restrictive for your intended usage, please contact the maintainer. | ||
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| ## Research notice | ||
| Please note that this repository is participating in a study into sustainability | ||
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| For more information, please visit | ||
| [our informational page](https://sustainable-open-science-and-software.github.io/) or download our [participant information sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf). | ||
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| <hr/> | ||
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| <b id="f1">1</b> : Monier B, Gettings M, Gay G, Mangeat T, Schott S, Guarner A, Suzanne M. Apico-basal forces exerted by apoptotic cells drive epithelium folding. Nature. 2015 doi: [10.1038/nature14152](https://doi.org/10.1038/nature14152) [↩](#a1) | ||
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