The SimCellDesigner is an interactive tool to design cell geometries for use with Simmune simulations. It is most suitable for geometries of simple to medium complexity, including compartments containing multiple interacting cells. The cell design process is centered around the concept of blobs or meta-balls. Each blob or meta-ball is a source of a spherical building block (or a sphere of influence) that can add it's strength to the final shape which is the sum of all building blocks with a smooth transition between blocks.
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Illustration of the meta-ball concept. Each of the colored objects is composed of two meta-balls. The distance between the meta-balls within one object increases from left to right. Observe the smooth transition between the meta-balls.
In biological terms a collection of meta-balls would be a cell. Each meta-ball by itself could be interpreted as a protrusion of a cell.
Note
Each "protrusion" corresponds to a meta-ball, or in other words a building block of the cell geometry. There is not necessarily a correspondence between compartments or regions of a biological cell and meta-balls. Given a large central meta-ball and several smaller meta-balls extending from it the smaller meta-balls could have an interpretation as a protrusion such as a lamelipod. Each meta-ball contributes to the cell shape in the same manner independently of the order in which they were added. Even if a model cell consists of a single meta-ball we will call this a protrusion in order to keep a simple yet suggestive naming scheme.
The SimCelldesigner allows multiple cells within a compartment. Meta-balls in different cells do not add their strength. If cells are in contact with each other a point in space that is influenced by meta-balls in different cells is considered to be part of the cell that exerts the stronger influence.