├── .esdoc.json ├── .eslintrc.js ├── .gitignore ├── ChangeLog ├── DOCS-README.txt ├── LICENSE ├── Makefile ├── README.md ├── TODO.txt ├── app ├── automatic-index.bash ├── include-list.txt ├── index.js └── manual-index.js ├── benchmarks ├── .gitignore ├── 2019-10-03-12-36.txt ├── Makefile ├── collective-migration.js ├── epidermis-with-tcells.js ├── epidermis.js ├── ising-model-3d.js ├── ising-model.js └── plot-exec.R ├── dev-src ├── grid │ └── HexGrid2D.js └── hamiltonian │ └── TunablePerimeterConstraint.js ├── docs ├── .gitignore ├── Makefile ├── ast │ └── source │ │ ├── .external-ecmascript.js.json │ │ ├── Canvas.js.json │ │ ├── DiceSet.js.json │ │ ├── cells │ │ ├── Cell.js.json │ │ └── Divider.js.json │ │ ├── converter │ │ ├── ArtistooImport.js.json │ │ ├── ArtistooWriter.js.json │ │ ├── ModelDescription.js.json │ │ ├── MorpheusImport.js.json │ │ ├── MorpheusWriter.js.json │ │ └── Writer.js.json │ │ ├── grid │ │ ├── CoarseGrid.js.json │ │ ├── Grid.js.json │ │ ├── Grid2D.js.json │ │ ├── Grid3D.js.json │ │ ├── GridManipulator.js.json │ │ └── grid-typedef.js.json │ │ ├── hamiltonian │ │ ├── ActivityConstraint.js.json │ │ ├── ActivityMultiBackground.js.json │ │ ├── Adhesion.js.json │ │ ├── AttractionPointConstraint.js.json │ │ ├── AutoAdderConfig.js.json │ │ ├── BarrierConstraint.js.json │ │ ├── BorderConstraint.js.json │ │ ├── ChemotaxisConstraint.js.json │ │ ├── ConnectivityConstraint.js.json │ │ ├── Constraint.js.json │ │ ├── HardConstraint.js.json │ │ ├── HardVolumeRangeConstraint.js.json │ │ ├── LocalConnectivityConstraint.js.json │ │ ├── ParameterChecker.js.json │ │ ├── PerimeterConstraint.js.json │ │ ├── PersistenceConstraint.js.json │ │ ├── PreferredDirectionConstraint.js.json │ │ ├── SoftConnectivityConstraint.js.json │ │ ├── SoftConstraint.js.json │ │ ├── SoftLocalConnectivityConstraint.js.json │ │ ├── VolumeConstraint.js.json │ │ └── constraint-typedef.js.json │ │ ├── models │ │ ├── CA.js.json │ │ ├── CPM.js.json │ │ ├── CPMEvol.js.json │ │ ├── GridBasedModel.js.json │ │ └── model-typedefs.js.json │ │ ├── simulation │ │ └── Simulation.js.json │ │ └── stats │ │ ├── BorderPixelsByCell.js.json │ │ ├── CellNeighborList.js.json │ │ ├── Centroids.js.json │ │ ├── CentroidsWithTorusCorrection.js.json │ │ ├── ConnectedComponentsByCell.js.json │ │ ├── ConnectedComponentsByCellBorder.js.json │ │ ├── Connectedness.js.json │ │ ├── PixelsByCell.js.json │ │ ├── Stat.js.json │ │ └── stat-typedef.js.json ├── badge.svg ├── class │ └── src │ │ ├── Canvas.js~Canvas.html │ │ ├── DiceSet.js~DiceSet.html │ │ ├── cells │ │ ├── Cell.js~Cell.html │ │ └── Divider.js~Divider.html │ │ ├── converter │ │ ├── ArtistooImport.js~ArtistooImport.html │ │ ├── ArtistooWriter.js~ArtistooWriter.html │ │ ├── ModelDescription.js~ModelDescription.html │ │ ├── MorpheusImport.js~MorpheusImport.html │ │ ├── MorpheusWriter.js~MorpheusWriter.html │ │ └── Writer.js~Writer.html │ │ ├── grid │ │ ├── CoarseGrid.js~CoarseGrid.html │ │ ├── Grid.js~Grid.html │ │ ├── Grid2D.js~Grid2D.html │ │ ├── Grid3D.js~Grid3D.html │ │ └── GridManipulator.js~GridManipulator.html │ │ ├── hamiltonian │ │ ├── ActivityConstraint.js~ActivityConstraint.html │ │ ├── ActivityMultiBackground.js~ActivityMultiBackground.html │ │ ├── Adhesion.js~Adhesion.html │ │ ├── AttractionPointConstraint.js~AttractionPointConstraint.html │ │ ├── BarrierConstraint.js~BarrierConstraint.html │ │ ├── BorderConstraint.js~BorderConstraint.html │ │ ├── ChemotaxisConstraint.js~ChemotaxisConstraint.html │ │ ├── ConnectivityConstraint.js~ConnectivityConstraint.html │ │ ├── Constraint.js~Constraint.html │ │ ├── HardConstraint.js~HardConstraint.html │ │ ├── HardVolumeRangeConstraint.js~HardVolumeRangeConstraint.html │ │ ├── LocalConnectivityConstraint.js~LocalConnectivityConstraint.html │ │ ├── ParameterChecker.js~ParameterChecker.html │ │ ├── PerimeterConstraint.js~PerimeterConstraint.html │ │ ├── PersistenceConstraint.js~PersistenceConstraint.html │ │ ├── PreferredDirectionConstraint.js~PreferredDirectionConstraint.html │ │ ├── SoftConnectivityConstraint.js~SoftConnectivityConstraint.html │ │ ├── SoftConstraint.js~SoftConstraint.html │ │ ├── SoftLocalConnectivityConstraint.js~SoftLocalConnectivityConstraint.html │ │ └── VolumeConstraint.js~VolumeConstraint.html │ │ ├── models │ │ ├── CA.js~CA.html │ │ ├── CPM.js~CPM.html │ │ ├── CPMEvol.js~CPMEvol.html │ │ └── GridBasedModel.js~GridBasedModel.html │ │ ├── simulation │ │ └── Simulation.js~Simulation.html │ │ └── stats │ │ ├── BorderPixelsByCell.js~BorderPixelsByCell.html │ │ ├── CellNeighborList.js~CellNeighborList.html │ │ ├── Centroids.js~Centroids.html │ │ ├── CentroidsWithTorusCorrection.js~CentroidsWithTorusCorrection.html │ │ ├── ConnectedComponentsByCell.js~ConnectedComponentsByCell.html │ │ ├── ConnectedComponentsByCellBorder.js~ConnectedComponentsByCellBorder.html │ │ ├── Connectedness.js~Connectedness.html │ │ ├── PixelsByCell.js~PixelsByCell.html │ │ └── Stat.js~Stat.html ├── converter.html ├── converter │ ├── artistoo2morpheus.html │ ├── modelStyle.css │ ├── morpheus-examples │ │ ├── cellsorting.xml │ │ └── protrusion.xml │ ├── morpheus2artistoo.html │ └── style.css ├── coverage.json ├── css │ ├── examples.css │ ├── explorable.css │ ├── github.css │ ├── identifiers.css │ ├── manual-page.css │ ├── manual.css │ ├── prettify-tomorrow.css │ ├── search.css │ ├── source.css │ ├── style.css │ └── test.css ├── examples.html ├── examples │ ├── ActModel.html │ ├── ActModelCustomStat.html │ ├── ActModelInteractive.html │ ├── ActOnMicroPattern.html │ ├── CancerInvasion.html │ ├── Canvas3D.js │ ├── CellDivision.html │ ├── Cellsorting.html │ ├── Chemotaxis.html │ ├── CollectiveMigration.html │ ├── Diffusion.html │ ├── DiffusionLimitedAggregation.html │ ├── DirectedMotionLinear.html │ ├── DirectedMotionTargetPoint.html │ ├── Epidermis.html │ ├── EpidermisWithTCells.html │ ├── EpithelialSheet.html │ ├── FakeMicroscopy.html │ ├── GameOfLife.html │ ├── IsingModel.html │ ├── ManyCellsDiffusion.html │ ├── ManyCellsPrefDir.html │ ├── Microchannel.html │ ├── NoTorusDemo.html │ ├── OrbitControls.js │ ├── RandomWalk.html │ ├── SIR.html │ ├── SingleCell.html │ ├── SuperCells.html │ ├── artistoo.js │ ├── colormap.js │ ├── cpm3d.html │ ├── fpsmeter.min.js │ ├── sliders.js │ ├── stochasticCorrector.html │ └── style.css ├── explorables.html ├── explorables │ ├── Explorable-ActModel.html │ ├── Explorable-CPM.html │ ├── Explorable-CellDivision.html │ ├── Explorable-CellSorting.html │ ├── Explorable-GameOfLife.html │ └── asset │ │ ├── frame-actbasic.html │ │ ├── frame-actfull.html │ │ ├── frame-adhesion-basic.html │ │ ├── frame-adhesion-multi.html │ │ ├── frame-basic.html │ │ ├── frame-division.html │ │ ├── frame-gol-large.html │ │ ├── frame-gol.html │ │ ├── frame-gol2.html │ │ ├── frame-gridstate-dynamic.html │ │ ├── frame-gridstate.html │ │ ├── frame-gridstate2.html │ │ ├── frame-ising.html │ │ ├── frame-metropolis.html │ │ ├── frame-obstacles.html │ │ ├── frame-perimeter.html │ │ ├── frame-singlecell.html │ │ ├── frame-sorting.html │ │ └── frame-volume.html ├── file │ └── src │ │ ├── Canvas.js.html │ │ ├── DiceSet.js.html │ │ ├── cells │ │ ├── Cell.js.html │ │ └── Divider.js.html │ │ ├── converter │ │ ├── ArtistooImport.js.html │ │ ├── ArtistooWriter.js.html │ │ ├── ModelDescription.js.html │ │ ├── MorpheusImport.js.html │ │ ├── MorpheusWriter.js.html │ │ └── Writer.js.html │ │ ├── grid │ │ ├── CoarseGrid.js.html │ │ ├── Grid.js.html │ │ ├── Grid2D.js.html │ │ ├── Grid3D.js.html │ │ ├── GridManipulator.js.html │ │ └── grid-typedef.js.html │ │ ├── hamiltonian │ │ ├── ActivityConstraint.js.html │ │ ├── ActivityMultiBackground.js.html │ │ ├── Adhesion.js.html │ │ ├── AttractionPointConstraint.js.html │ │ ├── AutoAdderConfig.js.html │ │ ├── BarrierConstraint.js.html │ │ ├── BorderConstraint.js.html │ │ ├── ChemotaxisConstraint.js.html │ │ ├── ConnectivityConstraint.js.html │ │ ├── Constraint.js.html │ │ ├── HardConstraint.js.html │ │ ├── HardVolumeRangeConstraint.js.html │ │ ├── LocalConnectivityConstraint.js.html │ │ ├── ParameterChecker.js.html │ │ ├── PerimeterConstraint.js.html │ │ ├── PersistenceConstraint.js.html │ │ ├── PreferredDirectionConstraint.js.html │ │ ├── SoftConnectivityConstraint.js.html │ │ ├── SoftConstraint.js.html │ │ ├── SoftLocalConnectivityConstraint.js.html │ │ ├── VolumeConstraint.js.html │ │ └── constraint-typedef.js.html │ │ ├── models │ │ ├── CA.js.html │ │ ├── CPM.js.html │ │ ├── CPMEvol.js.html │ │ ├── GridBasedModel.js.html │ │ └── model-typedefs.js.html │ │ ├── simulation │ │ └── Simulation.js.html │ │ └── stats │ │ ├── BorderPixelsByCell.js.html │ │ ├── CellNeighborList.js.html │ │ ├── Centroids.js.html │ │ ├── CentroidsWithTorusCorrection.js.html │ │ ├── ConnectedComponentsByCell.js.html │ │ ├── ConnectedComponentsByCellBorder.js.html │ │ ├── Connectedness.js.html │ │ ├── PixelsByCell.js.html │ │ ├── Stat.js.html │ │ └── stat-typedef.js.html ├── identifiers.html ├── image │ ├── badge.svg │ ├── examples │ │ ├── 3D.png │ │ ├── ActOnMicroPattern.gif │ │ ├── CancerInvasion.gif │ │ ├── Chemotaxis.gif │ │ ├── CollectiveMigration.gif │ │ ├── Diffusion.gif │ │ ├── DiffusionLimitedAggregation.gif │ │ ├── DirectedMotionLinear.gif │ │ ├── DirectedMotionTargetPoint.gif │ │ ├── Epidermis.gif │ │ ├── EpidermisWithTCells.gif │ │ ├── EpithelialSheet.gif │ │ ├── FakeMicroscopy.png │ │ ├── GameOfLife.gif │ │ ├── IsingModel.gif │ │ ├── ManyCellsDiffusion.gif │ │ ├── ManyCellsPrefDir.gif │ │ ├── RandomWalk.gif │ │ ├── SIR.gif │ │ ├── SingleCell.gif │ │ ├── StochasticCorrector.gif │ │ ├── SuperCells.gif │ │ ├── actmodel.gif │ │ ├── algorithm.gif │ │ ├── celldivision.gif │ │ ├── cellsorting.gif │ │ └── microchannel.gif │ ├── general │ │ ├── cpm-01.jpg │ │ ├── cpm-01.png │ │ ├── cpm-02.png │ │ ├── cpm-03.png │ │ └── cpm-04.png │ ├── github.png │ └── manual-badge.svg ├── index.html ├── index.json ├── layout.html ├── lint.json ├── manual │ ├── addConstraints.html │ ├── asset │ │ ├── ActSmall.html │ │ ├── ActSmall2.html │ │ ├── Cellsorting.html │ │ ├── ColorEx.html │ │ ├── Epidermis.html │ │ ├── IsingModel.html │ │ ├── SingleCell.html │ │ ├── artistoo.js │ │ ├── fpsmeter.min.js │ │ ├── github-repo.png │ │ ├── github-repo2.png │ │ └── perimeterExample.html │ ├── custommodules.html │ ├── getting-started.html │ ├── htmlTemplate.html │ ├── index.html │ ├── sharingSimulations.html │ ├── simulationConfig.html │ ├── simulationConfig2.html │ └── your-first-simulation.html ├── script │ ├── inherited-summary.js │ ├── inner-link.js │ ├── jquery.touchSwipe.min.js │ ├── patch-for-local.js │ ├── prettify │ │ ├── Apache-License-2.0.txt │ │ └── prettify.js │ ├── pretty-print.js │ ├── search.js │ ├── search_index.js │ ├── swipe-nav.js │ └── test-summary.js ├── source.html ├── test-file │ └── spec │ │ ├── CanvasSpec.js.html │ │ ├── DiceSetSpec.js.html │ │ ├── grid │ │ ├── Grid2DSpec.js.html │ │ ├── Grid3DSpec.js.html │ │ ├── GridExtensionSpec.js.html │ │ ├── GridManipulatorSpec.js.html │ │ └── GridSpec.js.html │ │ ├── hamiltonian │ │ ├── LocalConnectivityConstraintSpec.js.html │ │ ├── PerimeterConstraintSpec.js.html │ │ ├── PersistenceConstraintSpec.js.html │ │ └── SoftLocalConnectivityConstraintSpec.js.html │ │ ├── models │ │ └── CPMSpec.js.html │ │ └── simulation │ │ └── SimulationSpec.js.html ├── test.html ├── typedef │ └── index.html └── variable │ └── index.html ├── esdoc-template-artistoo ├── .gitignore ├── class.html ├── css │ ├── examples.css │ ├── explorable.css │ ├── github.css │ ├── identifiers.css │ ├── manual-page.css │ ├── manual.css │ ├── prettify-tomorrow.css │ ├── search.css │ ├── source.css │ ├── style.css │ └── test.css ├── details.html ├── file.html ├── identifiers.html ├── image │ ├── badge.svg │ └── manual-badge.svg ├── index.html ├── layout.html ├── manual.html ├── manualCardIndex.html ├── manualIndex.html ├── nav.html ├── properties.html ├── script │ ├── inherited-summary.js │ ├── inner-link.js │ ├── jquery.touchSwipe.min.js │ ├── patch-for-local.js │ ├── prettify │ │ ├── Apache-License-2.0.txt │ │ └── prettify.js │ ├── pretty-print.js │ ├── search.js │ ├── swipe-nav.js │ └── test-summary.js ├── single.html ├── source.html ├── summary.html ├── test.html └── testInterface.html ├── examples ├── .gitignore ├── 3D │ ├── Canvas3D.js │ ├── OrbitControls.js │ ├── artistoo.js │ ├── cpm3d.html │ ├── fpsmeter.min.js │ ├── ising-model-3d.js │ ├── ising.png │ ├── randomwalk3d.html │ └── randomwalk3d.js ├── build-examples │ ├── Makefile │ ├── extract-description.awk │ ├── extract-require.awk │ ├── new-simple.bash │ ├── new-simulation.bash │ ├── simulation-files │ │ ├── ActModel.js │ │ ├── ActModelCustomStat.js │ │ ├── ActOnMicroPattern.js │ │ ├── CancerInvasion.js │ │ ├── CellDivision.js │ │ ├── Cellsorting.js │ │ ├── Chemotaxis.js │ │ ├── CollectiveMigration.js │ │ ├── Diffusion.js │ │ ├── DiffusionLimitedAggregation.js │ │ ├── DirectedMotionLinear.js │ │ ├── DirectedMotionTargetPoint.js │ │ ├── Epidermis.js │ │ ├── EpidermisWithTCells.js │ │ ├── EpithelialSheet.js │ │ ├── GameOfLife.js │ │ ├── IsingModel.js │ │ ├── ManyCellsDiffusion.js │ │ ├── ManyCellsPrefDir.js │ │ ├── Microchannel.js │ │ ├── NoTorusDemo.js │ │ ├── RandomWalk.js │ │ ├── SIR.js │ │ ├── SingleCell.js │ │ ├── StochasticCorrector.js │ │ ├── SuperCells.js │ │ ├── Template.js │ │ └── TemplateSimple.js │ ├── write-example-html.bash │ ├── write-example-node.bash │ ├── write-html.bash │ ├── write-node.bash │ ├── write-simple-html.bash │ └── write-simple-node.bash ├── fpsmeter.min.js ├── html │ ├── ActModel.html │ ├── ActModelCustomStat.html │ ├── ActModelInteractive.html │ ├── ActOnMicroPattern.html │ ├── CancerInvasion.html │ ├── CellDivision.html │ ├── Cellsorting.html │ ├── Chemotaxis.html │ ├── CollectiveMigration.html │ ├── Diffusion.html │ ├── DiffusionLimitedAggregation.html │ ├── DirectedMotionLinear.html │ ├── DirectedMotionTargetPoint.html │ ├── Epidermis.html │ ├── EpidermisWithTCells.html │ ├── EpithelialSheet.html │ ├── FakeMicroscopy.html │ ├── GameOfLife.html │ ├── IsingModel.html │ ├── ManyCellsDiffusion.html │ ├── ManyCellsPrefDir.html │ ├── Microchannel.html │ ├── NoTorusDemo.html │ ├── RandomWalk.html │ ├── SIR.html │ ├── SingleCell.html │ ├── StochasticCorrector.html │ ├── SuperCells.html │ ├── artistoo.js │ ├── colormap.js │ ├── fpsmeter.min.js │ ├── sliders.js │ └── style.css └── node │ ├── .gitignore │ ├── colormap-cjs.js │ ├── run-ActModel.js │ ├── run-ActModelCustomStat.js │ ├── run-ActOnMicroPattern.js │ ├── run-CancerInvasion.js │ ├── run-CellDivision.js │ ├── run-Cellsorting.js │ ├── run-Chemotaxis.js │ ├── run-CollectiveMigration.js │ ├── run-Diffusion.js │ ├── run-DiffusionLimitedAggregation.js │ ├── run-DirectedMotionLinear.js │ ├── run-DirectedMotionTargetPoint.js │ ├── run-Epidermis.js │ ├── run-EpidermisWithTCells.js │ ├── run-EpithelialSheet.js │ ├── run-GameOfLife.js │ ├── run-IsingModel.js │ ├── run-ManyCellsDiffusion.js │ ├── run-ManyCellsPrefDir.js │ ├── run-Microchannel.js │ ├── run-NoTorusDemo.js │ ├── run-RandomWalk.js │ ├── run-SIR.js │ ├── run-SingleCell.js │ ├── run-StochasticCorrector.js │ └── run-SuperCells.js ├── misc ├── build-makeout.bash ├── cpm-01.jpg └── run-tests.bash ├── mustache-web ├── .gitignore ├── Makefile ├── data │ └── site.json ├── index.js ├── package-lock.json ├── package.json ├── partials │ ├── explorables │ │ ├── Explorable-ActModel.html │ │ ├── Explorable-CPM.html │ │ ├── Explorable-CellDivision.html │ │ ├── Explorable-CellSorting.html │ │ └── Explorable-GameOfLife.html │ ├── footer.html │ ├── head.html │ ├── manual │ │ ├── addConstraints.html │ │ ├── custommodules.html │ │ ├── getting-started.html │ │ ├── htmlTemplate.html │ │ ├── index.html │ │ ├── sharingSimulations.html │ │ ├── simulationConfig.html │ │ ├── simulationConfig2.html │ │ └── your-first-simulation.html │ └── nav.html ├── sources │ ├── converter │ │ ├── artistoo2morpheus.html │ │ ├── modelStyle.css │ │ ├── morpheus-examples │ │ │ ├── cellsorting.xml │ │ │ └── protrusion.xml │ │ ├── morpheus2artistoo.html │ │ └── style.css │ ├── explorable-assets │ │ ├── frame-actbasic.html │ │ ├── frame-actfull.html │ │ ├── frame-adhesion-basic.html │ │ ├── frame-adhesion-multi.html │ │ ├── frame-basic.html │ │ ├── frame-division.html │ │ ├── frame-gol-large.html │ │ ├── frame-gol.html │ │ ├── frame-gol2.html │ │ ├── frame-gridstate-dynamic.html │ │ ├── frame-gridstate.html │ │ ├── frame-gridstate2.html │ │ ├── frame-ising.html │ │ ├── frame-metropolis.html │ │ ├── frame-obstacles.html │ │ ├── frame-perimeter.html │ │ ├── frame-singlecell.html │ │ ├── frame-sorting.html │ │ └── frame-volume.html │ ├── images │ │ ├── examples │ │ │ ├── 3D.png │ │ │ ├── ActOnMicroPattern.gif │ │ │ ├── CollectiveMigration.gif │ │ │ ├── Diffusion.gif │ │ │ ├── DiffusionLimitedAggregation.gif │ │ │ ├── DirectedMotionLinear.gif │ │ │ ├── DirectedMotionTargetPoint.gif │ │ │ ├── Epidermis.gif │ │ │ ├── EpidermisWithTCells.gif │ │ │ ├── EpithelialSheet.gif │ │ │ ├── GameOfLife.gif │ │ │ ├── IsingModel.gif │ │ │ ├── ManyCellsDiffusion.gif │ │ │ ├── ManyCellsPrefDir.gif │ │ │ ├── RandomWalk.gif │ │ │ ├── SIR.gif │ │ │ ├── SingleCell.gif │ │ │ ├── StochasticCorrector.gif │ │ │ ├── SuperCells.gif │ │ │ ├── actmodel.gif │ │ │ ├── algorithm.gif │ │ │ ├── cancerinvasion.gif │ │ │ ├── celldivision.gif │ │ │ ├── cellsorting.gif │ │ │ ├── chemotaxis.gif │ │ │ ├── fakemicroscopy.png │ │ │ └── microchannel.gif │ │ ├── general │ │ │ ├── cpm-01.jpg │ │ │ ├── cpm-01.png │ │ │ ├── cpm-02.png │ │ │ ├── cpm-03.png │ │ │ └── cpm-04.png │ │ └── icons │ │ │ ├── github.png │ │ │ └── search.png │ └── manual │ │ └── asset │ │ ├── ActSmall.html │ │ ├── ActSmall2.html │ │ ├── Cellsorting.html │ │ ├── ColorEx.html │ │ ├── Epidermis.html │ │ ├── IsingModel.html │ │ ├── SingleCell.html │ │ ├── artistoo.js │ │ ├── fpsmeter.min.js │ │ ├── github-repo.png │ │ ├── github-repo2.png │ │ └── perimeterExample.html └── templates │ ├── blank.mustache │ ├── converter.mustache │ ├── examples.mustache │ ├── explorablepage.mustache │ ├── explorables.mustache │ ├── index.mustache │ ├── layout.mustache │ └── manualpage.mustache ├── mytemplate ├── class.html ├── css │ ├── github.css │ ├── identifiers.css │ ├── manual.css │ ├── prettify-tomorrow.css │ ├── search.css │ ├── source.css │ ├── style.css │ └── test.css ├── details.html ├── file.html ├── identifiers.html ├── image │ ├── badge.svg │ ├── esdoc-logo-mini-black.png │ ├── esdoc-logo-mini.png │ ├── manual-badge.svg │ └── search.png ├── index.html ├── layout.html ├── layout2.html ├── manual.html ├── manualCardIndex.html ├── manualIndex.html ├── nav.html ├── properties.html ├── script │ ├── inherited-summary.js │ ├── inner-link.js │ ├── patch-for-local.js │ ├── prettify │ │ ├── Apache-License-2.0.txt │ │ └── prettify.js │ ├── pretty-print.js │ ├── search.js │ └── test-summary.js ├── single.html ├── source.html ├── summary.html ├── test.html └── testInterface.html ├── package.json ├── rollup.config.js ├── spec ├── CanvasSpec.js ├── DiceSetSpec.js ├── TODO ├── grid │ ├── Grid2DSpec.js │ ├── Grid3DSpec.js │ ├── GridExtensionSpec.js │ ├── GridManipulatorSpec.js │ └── GridSpec.js ├── hamiltonian │ ├── LocalConnectivityConstraintSpec.js │ ├── PerimeterConstraintSpec.js │ ├── PersistenceConstraintSpec.js │ └── SoftLocalConnectivityConstraintSpec.js ├── helpers │ └── jasmine_examples │ │ └── SpecHelper.js ├── models │ └── CPMSpec.js ├── simulation │ └── SimulationSpec.js └── support │ └── jasmine.json ├── src ├── Canvas.js ├── DiceSet.js ├── cells │ ├── Cell.js │ └── Divider.js ├── converter │ ├── ArtistooImport.js │ ├── ArtistooWriter.js │ ├── ModelDescription.js │ ├── MorpheusImport.js │ ├── MorpheusWriter.js │ └── Writer.js ├── grid │ ├── CoarseGrid.js │ ├── Grid.js │ ├── Grid2D.js │ ├── Grid3D.js │ ├── GridManipulator.js │ └── grid-typedef.js ├── hamiltonian │ ├── ActivityConstraint.js │ ├── ActivityMultiBackground.js │ ├── Adhesion.js │ ├── AttractionPointConstraint.js │ ├── AutoAdderConfig.js │ ├── BarrierConstraint.js │ ├── BorderConstraint.js │ ├── ChemotaxisConstraint.js │ ├── ConnectivityConstraint.js │ ├── Constraint.js │ ├── HardConstraint.js │ ├── HardVolumeRangeConstraint.js │ ├── LocalConnectivityConstraint.js │ ├── ParameterChecker.js │ ├── PerimeterConstraint.js │ ├── PersistenceConstraint.js │ ├── PreferredDirectionConstraint.js │ ├── SoftConnectivityConstraint.js │ ├── SoftConstraint.js │ ├── SoftLocalConnectivityConstraint.js │ ├── VolumeConstraint.js │ └── constraint-typedef.js ├── models │ ├── CA.js │ ├── CPM.js │ ├── CPMEvol.js │ ├── GridBasedModel.js │ └── model-typedefs.js ├── simulation │ └── Simulation.js └── stats │ ├── BorderPixelsByCell.js │ ├── CellNeighborList.js │ ├── Centroids.js │ ├── CentroidsWithTorusCorrection.js │ ├── ConnectedComponentsByCell.js │ ├── ConnectedComponentsByCellBorder.js │ ├── Connectedness.js │ ├── PixelsByCell.js │ ├── Stat.js │ └── stat-typedef.js ├── unittests └── grid3d.js ├── video-capture ├── make-video.sh ├── 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