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--- examples:cellular_potts [16:30 11.11.2014] – Walter
+++ examples:cellular_potts [17:35 18.08.2021] (current) – Moved to GitLab Pages Diego Jahn
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-~~NOTOC~~
-==== Cellular Potts models ====
-==== Differential Adhesion: cell sorting in two dimensions ====
-[{{ :example-cellsorting2D.png?direct&200|Yellow cells engulf the red cells as a result of differential adhesion}}]
-{{vimeo>47171579? small}}
-=== Introduction ===
-This model shows the original cellular Potts model (a.k.a. Glazier-Graner model) of cell sorting based on the Steinberg's differential adhesion hypothesis.
-=== Model description ===
-Two ''CellTypes'' are defined, each of which has a ''VolumeConstraint'' specifying the cell's target area/volume. In the ''CPM'' element, the ''MetropolisKinetics'' can be configured and the ''Interaction'' energies between cell types are specified.
-Although cells can be initialized as single points using e.g. the ''InitCircle'' plugin, in this example, the ''Nodes'' of each ''Cell'' in the ''CellPopulations'' are given explicitly. In fact, these ''Populations'' are restored results of a previous simulation.
-The simulation shows two populations of spatially resolved cells that initially organized in a mosaic fashion. Through differential adhesion, the motile cells sort out and re-organize into an distribution in which one cell type engulfes the other.
-Snapshots of the simulation are saved to files named [Title][Time].xml.gz. These files containing intermediate and result states can be opened and used as initial conditions for new simulations. Remember to change ''StartTime'' and ''StopTime'' accordingly.
-=== Model ===
-<code xml |h CellSorting_2D.xml |h>
-extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/CellSorting_2D.xml
-</code>
-In Morpheus GUI: ''Examples -> CPM -> CellSorting_2D.xml''
-=== Reference ===
-Graner F, Glazier J. [[http://dx.doi.org/10.1103%2FPhysRevLett.69.2013|Simulation of Biological Cell Sorting Using a Two-Dimensional Extended Potts Model]]. //Phys. Rev. Lett.// 69 (13): 2013–2016, 1992.
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-==== Proliferation in two dimensions ====
-[{{ :example_proliferation2d.png?direct&200|Growing cell population}}]
-{{vimeo>51689598? small}}
-=== Introduction ===
-This model show a simulation of a growing cell population, using the cellular Potts model.
-=== Model description ===
-This model specifies ''CellType'' which has a ''VolumeConstraint'' and a ''Proliferation'' plugin.
-In the ''Proliferation'' plugin, the ''Conditions'' for a cell to divide are given. Here, each cell that has more than 90% of the target volume has a small probability to divide. Once a division has taken place, the ''Equation'' defined in the ''Triggers'' elements are triggered.
-=== Model ===
-<code xml |h Proliferation_2D.xml |h>
-extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/Proliferation_2D.xml
-</code>
-In Morpheus GUI: ''Examples -> CPM -> Proliferation_2D.xml''
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-==== Persistence ====
-[{{ :examples:persistence.png?direct&200|Persistence of individual cells causes self-organized collective motion}}]
-{{vimeo>50699261? small}}
-=== Introduction ===
-This example shows self-organized collective motion of cells as a result of persistence ('cellular inertia'). A similar model has recently been used in ([[http://dx.doi.org/10.1088/1367-2630/15/7/075006|Czirok et al., 2013]]).
-=== Description ===
-The model uses the ''Persistence'' plugin that causes cells to prefer to move in their current direction. The direction is stored in a ''PropertyVector'' that is used to plot the color and arrows in ''Gnuplotter''.
-The model is simulated in a circular domain with constant boundary conditinos, which can be set up in ''Lattice / Domain / Circle''. The value for the constant boundary is specified in ''CPM / BoundaryValue''.
-=== Try it! ===
-  * Change the boundary conditions from circular=constant to x/y=periodic and observe the resulting collective motion.
-  * Change the ''decay-time'' of ''Persistence'' (specifying the 'memory').
-=== Model ===
-<code xml |h Persistence_2D.xml |h>
-extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/Persistence_2D.xml
-</code>
-In Morpheus GUI: ''Examples -> CPM -> Persistence_2D.xml''
-\\
-=== Reference ===
-Czirók A, Varga K, Mehes E, Szabo A, [[http://dx.doi.org/10.1088/1367-2630/15/7/075006|Collective cell streams in epithelial monolayers depend on cell adhesion]]. //New J. Phys.// 15 075006, 2013.
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-==== Proliferation in three dimensions ====
-[{{ :example-proliferation3d.png?direct&200|Cell population grown from single initial cell}}]
-{{vimeo>47313357? small}}
-=== Introduction ===
-This model show a CPM simulation of a growing cell population in 3D.
-=== Model description ===
-This model specifies ''CellType'' which has a ''VolumeConstraint'' and a ''Proliferation'' plugin.  In the ''Proliferation'' plugin, the ''Conditions'' for a cell to divide are given. Here, each cell that has more than 90% of the target volume has a small probability to divide. Once a division has taken place, the ''Equation'' defined in the ''Triggers'' elements are triggered.
-In this model, two ''medium'' cell types have been defined. One of these (called matrix) is used to represent a matrix with higher adhesivity. This is done by (1) defining the 'matrix' cell type as a ''BoundaryCondition'' of the -z boundary in the ''CPM'' and (2) providing lower contact energy for cell-matrix interaction than for cell-medium interactions.
-The simulation is visualized using the ''TiffPlotter'' that saves TIFF image stacks that can be loaded by image analysis software such as [[http://fiji.sc|Fiji]] and displayed using Fiji's 3D Viewer plugin.
-=== Model ===
-<code xml |h Proliferation_3D.xml |h>
-extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/Proliferation_3D.xml
-</code>
-In Morpheus GUI: ''Examples -> CPM -> Proliferation_3D.xml''
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-==== Run and Tumble ====
-[{{ :examples:runandtumble.png?direct&200|Modeling cell movements as a Levy walk}}]
-{{vimeo>111264192? small}}
-=== Introduction ===
-This example models a single cell that moves according to a Levy walk: a random walk with occassional occurrence of long straight walks.
-=== Model description ===
-The model defines a ''CPM'' cell that has two properties:
-  * A ''PropertyVector'' that gives the direction of movement and
-  * A ''Property'' that defines the time when this direction of movement is changed.
-The change in direction is using a ''VectorRule''. In this case, it specifies a new random direction for each of the 3 x,y,z coordinates separately: ''move_dir = sin(angle), cos(angle), 0'' where ''angle = rand_uni(0, 2*pi)''.
-This is calculated with an ''Event''. Upon triggering, this sets the new direction and a waiting time until the next change of direction. To model a superdiffusive Levy walk, this waiting time is chosen from an exponential distribution: ''change_time = time + 20 * rand_gamma(0.5, 5)''
-Finally, the cell is made to move in the chosen direction using ''DirectedMotion'' that takes the ''PropertyVector'' as input.
-=== Model ===
-<code xml |h RunAndTumble.xml |h>
-extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/RunAndTumble.xml
-</code>
-In Morpheus GUI: ''Examples -> CPM -> RunAndTumble.xml''
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-==== Stem cells in the intestinal crypt ====
-[{{ :crypt.png?direct&200|Asymmetric cell division and changing cell type}}]
-{{vimeo>111262100? small}}
-=== Introduction ===
-This illustrative example shows the emergence of clonal populations from stem cells in an intestinal crypt. Stem cells in the bottom of the crypt divide asymmetrically and produce a population of transit amplifying (TA) cells. For each of the TA cells, the color indicates the stem cell is it derived from.
-=== Model description ===
-This model shows several new modeling features, available as of Morpheus 1.2.
-== Loading domain from image ==
-The crypt-like domain is specified by loading an external 8-bit TIFF image file using ''Lattice/Domain/Image''.
-== Asymmetric cell division ==
-Stem cell divide asymmetrically using the new ''ChildID'' handles in the ''Proliferation'' plugin. This sets a user-defined symbol (here: daughter) to either 1 or 2 that can be used to distinguish both daughter cells. This symbol is then used to set the stemness ''s'' of one daughter to 1 and the other to 0: ''s = if(daughter==1, 1, 0)''.
-== Conditionally changing cell types ==
-When a cell looses its stemness ''s'', it is moved to the TA cell type. This is done using the new ''ChangeCellType'' plugin.
-Upon satisfyiug its ''Condition'', ''ChangeCellType'' move the cell to te specified new cell type. By default, all the properties of a cell that exist in both cell type context are maintained and nuspecified ones are set to their default values. This default behavior can be overridden in ''Triggers'' by specifying ''Rules'' stating how to deal with specific properties.
-== PopulationReporter ==
-The new ''PopulationReporter'' allows the collection of statistical data about the cell population. Here, it is used to count the sizes of the various clonal populations. This number of reported into a ''Global'' and subsequently written to file and plotted using a ''Logger''.
-=== Model ===
-<code xml |h Crypt.xml |h>
-extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/Crypt.xml
-</code>
-In Morpheus GUI: ''Examples -> CPM -> Crypt.xml''
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