The buttons window is organized hierarchically. The top level buttons apply to operations acting on the whole compartment. Lower level buttons relate to cells and their protrusions regions and nucleus.
Global operations
Load a previously saved geometry file.
Save the current geometry to a file. A geometry can only be saved to a file if each cell has exactly one connected component. A cell has one connected component if each volume element ot the cell (displayed as cubes) is either directly or indirectly connected to all other volume elements through a shared face. If saving is attempted if one or more cells do not have exactly one connected component a warning will be issued and saving is refused. SimCellDesigner will also attempt do discover unusual shapes that are usually unwanted. Such shapes are cells with cavities, and cells with one or more handles i.e. torus shaped cells.
Shows a contact address and lists the libraries used by the SimCellDesigner.
Compartment
Set the dimensions of the compartment. The minimal extend in each direction is one. The largest allowed extend is 90.
The linear size of a single volume element given in micro meter.
This button allows to set the length of the ruler in the 3d window to a certian length. The length of the ruler relative to the cell sizes wil not change. The only other value affected is the grid constant.
This checkbox toggles the visibility of the ruler in the 3d window. When the 3d window is active you can use the R key to toggle the ruler visibility.
A new cell with a single protrusion is created in placed in an empty location within the compartment.If there are no empty location the cell is placed at a location experiencing the least influence exerted by the protrusions.
Move alls cells such that cells are centered within the compartment.
Cell
Toggles the visibility of the cell. This allows to inspect the contact surface in cell - cell interactions, and helps to reduce clutter in settings with many cells. An invisible cell still influences other cells. It is just not drawn in the 3d display.
Each Cell in the SimCellDesigner has three differerent edit modes, which are described in detail below.
Displays the volume of the cell.
Displays the volume of the cell's nucleus.
Copies a cell including all of it's regions and nucleus. The copy of the cell will be moved to an unoccupied space in the compartment.
Deletes a cell including all of it's regions and nucleus.
Determines whether the cell's geometry or nucleus is edited or patitioned in regions. The avaiable buttons for interacting with a cell depend on the edit mode.
Geometry
Set the position of the cell within the compartment. Positions of protrusions, the nucleus and regions are relative to the cell, thus they will follow the movement of the cell.
Assign a name to a cell, used for identification during simulations.
In simulations with dynamic morphology this variable can be used to set the relaxed or resting volume of a cell, relative to the volume displayed in the SimCellDesigner. Setting this variable to values larger than one can for example be used to simulate osmotic swelling. For more information on dynamic morphologies refer to the Simulator's manual.
In simulations with dynamic morphology this variable can be used to set the relaxed or resting surface area of a cell, relative to the surface area displayed in the SimCellDesigner. Setting this variable to values larger than one can for example be used to simulate the increas of the cells surface area during cell migration. For more information on dynamic morphologies refer to the Simulator's manual
Add a new protrusion at the position of the cell's anchor point (i.e. the coordinates of the cell itself). The new protrusion might not be visible if other protrusions are already located in the same location. Simply move the protrusion in the desired direction and it will become visible.
Protrusions are the actual building blocks of model cells. The first "Protrusion" represents the body of the cell, therfore it lacks sliders for changing its position.
Set the position of the protrusion relative to the cell.
Change the radius of the protrusion. Negative values can be used to set up protrusions that "substract" from the rest of the cell to construct invaginations or cavitities.
Click to remove the protrusion from the cell.
Regions
Add a new region at the position of the cell's anchor point (i.e. the coordinates of the cell itself). The new region will be scaled to overlap most of the cell. Regions are exclusive, and only apply to the cell that is being edited.
Set the position of the region relative to the cell.
Change the radius of the region.
Click to remove the region from the cell.
Assign a name to a region, used for identification during simulations.
Nucleus
Add a new source of a meta ball contributing to the cell's nucleus at the position of the cell's anchor point (i.e. the coordinates of the cell itself).
Set the position of the nucleus relative to the cell.
Change the radius of the nucleus.
Click to remove the source term of the nucleus from the cell.
The 3d Display can be zoomed, panned and rotated using the mouse and keyboard. Use the actions in the list below to change the 3d Display:
Press RMB and drag vertically
Mouse-wheel
Press MMB and drag
Press Shift+LMB and drag
Press LMB and drag
Press Shift+LMB and drag to Roll