Section: New Software and Platforms

Platforms

TiQuant and TiSim The software for tissue image analysis (Tissue Quantifier) and simulation (Tissue Simulator) has been enriched. In more details,

TiQuant

TiQuant [94], [91] is implemented in portable object-oriented JSO C++. The GUI is based on QT and supports real-time visualisation using OpenGL. TiQuant is embedded in the tissue modelling framework CellSys and thus is tightly linked with TiSim, a versatile and efficient simulation environment for tissue models. TiQuant provides an interface to VolView and further complements its functionality by linking to the open-source libraries ITK and VTK (itk/vtk.org). The image/volume processing chains currently implemented in TiQuant for example include techniques to segment conduit and cell segmentation from 3D confocal micrographs of liver tissue based on the Adaptive Otsu Thresholding method and a number of morphological operators. TiQuant was currently extended by a machine-learning component, largely replacing the manual image-processing pipeline.

TiSim

TiSim permits agent-based simulations of multicellular systems. It is modular, in object-oriented ISO C++, the GUI based on Qt and OpenGL, while also allowing for batch mode runs. The software permits multi-scale simulations by integration of molecular pathways (for signalling, metabolisms, drug) into each individual cell. Applications so far are monolayer growth, multicellular spheroids, liver regeneration, TRAIL-treatment simulations. It has an SBML interface. In a largely finished follow-up version it will integrate a deformable cell model by triangulation of cell surface, deformable rod models, extracellular matrix and vascular flow and transport. TiSim can be directly fed by structures synthesised from processed image data from TiQuant.

Impact: The tool is used by our collaborators in liver biology, medicine and toxicology. We recently trained a PhD student from P. Segers (Ghent Univ.) on TiQuant and from T. Hillen (Univ. Alberta, Ca) on TiSim and organised a workshop on benchmarking and comparing agent-based models and tools (workshop Leipzig, volet 5).