Package: tyssue
tyssue : An epithelium simulation library[ANN] Working on a 1.0 releaseDear tyssue user or prospective user, I come with good bearings.This commit to the **new default branchmainis the official start of the 1.0 release. It is long overdue and there is a lot of house keeping.Short termfix CI w/ github actionsReadthedocs with mkdocTestsNotebook testsMerge PRs #263 #274TestsCheck Polarization notebooksNameDownloadsVersionPlatformsCoverageDocCHATtyssue is now published in the Journal of Open Source Software!ZENODO DOIJOSS DOIThetyssuelibrary seeks to provide a unified interface to implement
biomechanical models of living tissues.
It's main focus is onvertex based epithelium models.OverviewWhat kind of Models does it implement?The first model implemented is the one described in
Monier et al.1. 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 a
stage. They implement a description of the tissue's rheology, within a
dissipation function formalism.What kind of geometry does it model ?tyssueallows to model different geometries in 2D and in 3D.  Presentation of the different geometries and how to create them are shown in thisnotebook.General Structure of the modeling APIDesign principlesAPIs not appsEach 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 software follow an architecture
based on a core C++ engine with a combinaison of markup or scripting
capacities to run specific simulation.Intyssue, we rather try to expose an API that simplifies the
building of tissue models and running simulations, while keeping the
possibilities as open as possible.Separate structure, geometry and modelsWe seek to have a design as modular as possible, to allow the same
epithelium mesh to be fed to different physical models.Accessible, easy to use data structuresThe core of the tyssue library rests on two structures: a set ofpandas DataFrameholding the tissue geometry and associated data,
and nested dictionaries holding the model parameters, variables and
default values.The API thus defines anEpitheliumclass. An instance of this class
is a container for the datasets and the specifications, and implements
methods to manipulate indexing of the dataframes to ease calculations.The mesh structure is heavily inspired byCGAL Linear Cell Complexes,
most importantly, in the case of a 2D vertex sheet for example, each
junction edge between the cells is "splited" between two orientedhalf
edges.Creating an Epithelium## Core objectfromtyssueimportSheet## Simple 2D geometryfromtyssueimportPlanarGeometry## Visualisation (matplotlib based)fromtyssue.drawimportsheet_viewsheet=Sheet.planar_sheet_2d('basic2D',nx=6,ny=7,distx=1,disty=1)PlanarGeometry.update_all(sheet)sheet.sanitize()fig,ax=sheet_view(sheet)DocumentationThe documentation is now browsable ontyssue.ioThe old documentation is still browsable onlinehereIntroduction notebooks are availablehere.VisualisationThanks to @kephale, there is a napari plugin to visualise tyssue simulation output.
You can find ithere.What's new in 1.0 ?No collision in 2D (use effectorRepulsion)Add new geometry : 2D lateral geometryAdd mean calculation inEpitheliumAddsheetconversion tomeshfromMeshioAllow hole in 2D sheetFix some visualisationRoadmapYou are welcome to participate in the development ofTyssue.
What is planned for the future ofTyssue?Solve collision in 2.5D & 3DUse ZARR instead of HDF5 as base file formatUpgrade geometry creationCompound geometry to form complex shapeUse biological image as blueprintAdd rheology modelSwitch to github-action for continuous integrationMailing list:tyssue@framaliste.org-https://framalistes.org/sympa/info/tyssueSubscribe ➙https://framalistes.org/sympa/subscribe/tyssueUnsubscribe ➙https://framalistes.org/sympa/sigrequest/tyssueAuthorsBertrand Caré - @bcareCyprien Gay - @cypriengayGuillaume Gay (maintainer) - @glygHadrien Mary - @hadimFrançois MolinoMagali SuzanneSophie Theis - @sophietheisDependenciesAs 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...Show dependenciesCoreCGAL > 4.7Python >= 3.6numpyscipymatplotlibpandaspytablesjupyternotebookquantitiesipywidgetspythreejsipyvolumevispyTestspytestcoveragepytest-covInstallYou can install the library with the conda package managercondainstall-cconda-forgetyssueThrough PyPiYou can also install tyssue from PyPi, this is a CGAL-less version (pure python), lacking some features:python -m pip install --user --upgrade tyssueFrom sourceSeeINSTALL.mdfor a step by step install, including the necessary python environment.How to citeIf you findtyssueuseful please citethis repositoryusing its DOI as follows:Theis, Suzanne, Gay, (2021). Tyssue: an epithelium simulation library. Journal of Open Source Software, 6(62), 2973 doi:https://doi.org/10.21105/joss.02973Zenodo doi:10.5281/zenodo.4817609PublicationsIftyssuehas made a substantial contribution to your work, please edit this file and open a PR.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.130.108401Rahman T, Peters F and Wan LQ. Cell Jamming Regulates Epithelial Chiral Morphogenesis. J Biomech. 2023. doi:10.1016/j.jbiomech.2023.111435Fiorentino 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.1009552Related repository:https://github.com/ScialdoneLab/2DLEGICourcoubetis 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.1009952Martin 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.2021.01.005Related repository:https://github.com/suzannelab/polarityGracia 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/s41467-019-10720-0Related repository:https://github.com/suzannelab/invaginationMonier 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/nature14152Related repository:https://github.com/glyg/leg-jointLicenceSince version 0.3, this project is distributed under the terms of theGeneral Public Licence.Versions 2.4 and earlier were distributed under theMozilla Public Licence.If GPL licencing is too restrictive for your intended usage, please contact the maintainer.Research noticePlease note that this repository is participating in a study into sustainability
of open source projects. Data will be gathered about this repository for
approximately the next 12 months, starting from June 2021.Data collected will include number of contributors, number of PRs, time taken to
close/merge these PRs, and issues closed.For more information, please visitour informational pageor download ourparticipant information sheet.1: 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↩