An automated image analysis tool for quantitative studies of dynamic 3D-wound healing assays

• Applicant: Dr. Sabrina Roßberger
• Subject Area: Medical Physics, Biomedical Technology ; Biophysics
• Term: from 2016 to 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 317276344

An effective and fast wound healing process is essential for preserving the integrity of the skin and thus crucial for a functioning organism. Causes of skin damage are various including external physical force, surgery or diseases. Lately, 3-dimensional (3D) wound healing models have been successfully established. These are capable of revealing the complex interplay of different cell types during wound healing processes. However, visualization and analysis have only been performed on histological sections, which reveal only limited insights into the underlying dynamics.I will establish a 3D-in-vitro optical microscopy technique and a novel visualization workflow based on live-cell imaging and automated analysis routines to analyze the dynamic behavior of a whole in-vitro 3D-skin model. We will implement a recently for biological applications rediscovered imaging method - light sheet fluorescence microscopy (LSFM) - for time-lapse imaging. Thus, for the first time the fundamental underlying mechanism and dynamic aspects of wound healing demonstrated on an in-vitro 3D-skin model will be elucidated. Current 3D-tissue studies are lacking a common software tool for automated and comprehensive analysis of time resolved image data. Based on the expertise in our research group and of our collaboration partners we propose a software tool for automated and unbiased image analysis on a single cell level for whole in-vitro 3D-skin models and wound healing assays. Moreover, the developed algorithms are not limited to skin but can be easily adapted and applied to other tissue engineering experiments.Exploring the 3D-skin model the algorithm will allow for characterizing the healthy state of the skin in an unbiased manner based on well-defined extracted biophysical features. These features will be tracked over time and thus allow quantification of changes during the highly dynamical process of wound healing. Finally, we will establish the developed algorithms as an automated and unbiased benchmarking tool for high throughput screening (HTS) assays for testing the performance of various wound healing mediators and wound covers in in-vitro experiments.The proposed interdisciplinary project combines both biophysical studies on wound healing experiments and bioinformatics in order to develop a sophisticated and user-friendly bioinformatics tool for experimentalists.

• DFG Programme: Research Grants