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Multicellular FE & biochemical solver

This C++ software is intendent for the simulations of the multicelular systems in which the mechanical and biochemical signals can be coupled. It uses the Finite Element solver for the detailed decription of mechanics on the subcelular level and the ODE solver for the solution of the network of biochemical reactions on the scale of tye cell and wall compartments.
  • The both solvers can be interleaved and their variables and parameters coupled.
  • The package contains a library of rules for defining the various shapes of the cells and tissues in the artificial templates as well as the posibility of reading the externally prepared geometries or meshes obtained e.g. from experimental data.
  • It includes a simple hexahedral mesher and a convinient way of selecting mesh elements, faces, nodes, tissue compartments etc. with predefined or user specified predicates, which allows for the easy aplication of distributed or concentrated loads and the boundary conditions.
  • The output data is saved in the VTK format for the visualization with the external viewer.
The first version of this software was developed during my work at UC Irvine in Eric Mjolsness group. Later its functionality was extended and now it includes slightly modified "Organism" code, the multicelular biochemical reaction solver developed by Henrik Jönsson, Patrik Sahlin and Pontus Melke. The layout of the FE solver was inspired by the early versions of the DOLFIN package.

Mamalian embryo simulator

Aim of this C++ code is to provide a platform for simulating the mechanical and genetic interactions taking place in the early mamlian development. The blastomers are modeled as the incompressible elastic ellipsoids or spheres which can interact with each other and the pellucid zone coinstraining the whole embryo. The dynamics is solved with the use of 5-th order Runge-Kuta ODE solver.
  • The mechanical interactions consider the elastic, adhesion and viscous drag forces.
  • Each cell has a set of variables defining its state including the mechanical parameters, concentrations of various proteins, polarizarion vectors, cell cycle lenghts etc. These variables can evolve in the time according to the required equations or rules.
  • Cells can divide and partition their content in various ways depending on their state.


Costanza is a 3D segmentation and image quantification tool. It is primarily intended for the analysis of 3D image stacks form confocal microscopy, but it will work with any other type of image as well. It is implemented in Java as a plugin to the popular image manipulation program ImageJ. It uses 3D watershed segmentation algorithm and is optimized for speed so it can handle large 3D image stacks in reasonable time. The software and the user guide can be downloaded from Costanza web page