CompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in-silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D intuitive and make Virtual Tissue modeling accessible to users without extensive software development or programming experience.

It uses Cellular Potts Model to model cell behavior.

Tissue Cell Segmentation


This macro is meant to segment the cells of a multicellular tissue. It is written for images showing highly contrasted and uniformly stained cell membranes. The geometry of the cells and their organization is automatically extracted and exported to an ImageJ results table. This includes: Cell area, major, minor fitted ellipse radii + major axis orientation and number of neighbors of the cells. Manual correction of the automatic segmentation is supported (merge split cells, split merged cells).

Sample image data is available in the documentation page.