Morpheus

This model show a CPM simulation of a growing cell population in 3D.

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 Fiji and displayed using Fiji's 3D Viewer plugin.

extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/Proliferation_3D.xml

In Morpheus GUI: Examples → CPM → Proliferation_3D.xml

This example models a single cell that moves according to a Levy walk: a random walk with occassional occurrence of long straight walks.

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.

extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/RunAndTumble.xml

In Morpheus GUI: Examples → CPM → RunAndTumble.xml

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.

This model shows several new modeling features, available as of Morpheus 1.2.

The crypt-like domain is specified by loading an external 8-bit TIFF image file using Lattice/Domain/Image.

Stem cells divide asymmetrically using the new ChildID handles in the Proliferation plugin. This sets a user-defined symbol (here called daughter) to either 1 or 2. This symbol can then be used to distinguish both daughter cells and treat them differently. In this example, it used to set the stemness (s) of one daughter to 1 and the stemness of the other daughter cell to 0.

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 moves the cell to the specified new cell type. By default, all the properties of a cell that exist in both cell type context are maintained and unspecified ones are set to their default values. This default behavior can be overridden using Triggers that specify Rules stating how to deal with specific properties.

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.

extern>http://imc.zih.tu-dresden.de/morpheus/examples/CPM/Crypt.xml

In Morpheus GUI: Examples → CPM → Crypt.xml