Project 14

Design and implementation of workflow tools for multiplexed time-lapse imaging experiments in zebrafish screening

ESR14: Sankeert Satheesan

ACQUIFER Imaging (Germany)

Supervisor: Dr. J. Gehrig, co-supervisors: local: Prof. Dr. J. Wittbrodt, external: academic: N. Peyrieras (P7, CNRS)

Objectives: Modern automated microscopes allow multi-dimensional acquisition of numerous time-lapse experiments in a single run, but new tools, protocols & software are needed to fully exploit the technological possibilities of modern robotic microscopes for small vertebrates. Adding the temporal dimension to whole organism screening scenarios leads to increasingly complex imaging datasets causing analysis bottlenecks. We will address this lack of technology by (i) establishing new assays for advanced multiplexed time-lapse experiments, (ii) developing new imaging and workflow control tools, (iii) novel image analysis tools to analyse these very complex multidimensional datasets.

Results: 1) Novel protocols for long-term imaging including optimized anesthesia conditions and spatiotemporal sampling, 2) software tools for real-time and post-acquisition tracking of XYZ movements of regions of interest (e.g. object-based focusing) and event detection, 3) novel software tools with broad applicability for analysis of dynamic features such as heartbeat, cell and tissue migration, growth and regeneration.

Secondments: Academic: P6 Univ. Sheffield, Prof. S. Renshaw, Month 16, 1 month, Training on imaging inflammation in zebrafish, P4 STUBA, Prof. K. Mikula, Month 18, 2 months, Tracking algorithms and advanced segmentation techniques. Non-academic: P11 TatraMed, Dr. J. Urbán, Month 24, 1 month. Advanced image processing.