Under physiologic conditions in the organism, most cells live in a 3-D environment and not on a flat, smooth and hard 2-D plastic or glass surface. Over the past years, we have extensively used collagen-based 3-D biopolymer matrices for cell culture, and have devloped methods to characterize their structural and mechanical properties.
Licup AJ. Stress controls the mechanics of collagen networks. PNAS 2015 (PDF) Munster S. Strain history dependence of the nonlinear stress response of fibrin and collagen networks. PNAS 2013 (PDF) Lang NR. Estimating the 3D pore size distribution of biopolymer networks from directionally biased data. Biophys J 2013 (PDF) Krauss P. Parameter-Free Binarization and Skeletonization of Fiber Networks from Confocal Image Stacks. PloS one 2012 (PDF) Mickel W. Robust Pore Size Analysis of Filamentous Networks From 3D Confocal Microscopy. Biophys J 2008 (PDF)
Traction forces in 3-D are important, for instance, for the migration of cells (such as cancer cells, or immune cells) through the connective tissue. To measure forces, we extend ideas from 2-D traction microscopy to the third dimension. In analogy to 2-D traction microscopy, 3-D tractions can be calculated by measuring the 3-D deformation field of the connective tissue matrix surrounding a cell.
Butler JP. Traction fields, moments, and strain energy that cells exert on their surroundings. AJP 2001 (PDF) Koch TM. 3D Traction Forces in Cancer Cell Invasion. PloS one 2012 (PDF) Steinwachs J. Three-dimensional force microscopy of cells in biopolymer networks. Nature Methods 2016 (PDF)
We study the collective dynamics of penguin movements with image processing technologies adapted from cell migration and particle tracking. During the antarctic winter, emperor penguins have to sustain temperatures down to -50° Celsius combined with strong winds. To conserve energy, they move close together and share their body heat (huddling). Movements inside the huddle are highly coordinated so that every penguin gets to pass the warmest zone in the center of the huddle. We study how these huddles move, and how the penguins move inside the huddle, by taking time lapse images (every 1 sec) from an elevated position, and tracking the head of every single penguin for several hours.