Continuation of M3N

A large part of the software currently in use in the project-team was initiated and developed within former projects (Menusin, M3N).

CellSys

Participants : Géraldine Cellière [PhD student] , Dirk Drasdo [correspondent] , Stefan Höhme, Adrian Friebel [PhD student, University of Leipzig] , Tim Johann [Software Engineer, University of Leipzig] , Johannes Neitsch [PhD student] , Paul Van Liedekerke [Research Engineer] .

Based on an earlier submitted software (Hoehme and Drasdo, Bioinformatics, 2010) a modular computer simulation software for image analysis of tissue samples at histological scales, as well as for individual cell (agent)-based modeling of tumour and tissue growth, and tissue regeneration has been developed. Cell movement is solved either by systems of coupled equations of motion for each individual cell or by Kinetic Monte Carlo methods. The software uses a git framework to facilitate coordinated contributions of multiple developers. The image analysis part allows analysis of structures down to sub-cellular scale such as liver micro-capillaries and bile cannaliculi structures. So far, blood flow as well as growth and regeneration processes, fluxes of chemicals by diffusion and flow etc can be modelled, finite element solvers, ITK and VTK have been integrated.

The software CellSys is calibrated to allow use by external and internal researchers. The idea is to perspectively go open-source and offer consultancy for potential users.

Moreover in 2013 the image processing and analysis chain was refined to capture high resolution laser scanning micrographs. The algorithms were integrated into CELLSYS (see: software) and our experimental partner labs within the projects VLN and NOTOX were provided with the software to allow image analysis directly in their lab and with their people. Along the same line an experimental partner lab at the German Cancer center was provide with a small image analysis tool permitting them to efficiently analyze their bright field images on growing and invasive cancer cell populations in vitro (LUNGSYS).