Method Development for Microbial Ecology
Close-up view of a kChip filled with droplets in which growth of bacterial cells can be monitored at high-throughtput.
Developing and implementing new methods enables us to overcome existing limitations and obtain more accurate, comprehensive data. We are mostly working on methods, tools and software related to microfluidics and live-cell imaging, inluding:
- external page Midap, a pipeline for automated segmentation and tracking of bacterial cells in time-lapse microscopy image series; a selection of state-of-the-art segmentation and tracking methods are provided from which the user can select the most suited ones for their data. Available on external page github (MSE with MSE together with Franziska Oschmann, external page Janis Fluri and Lukas von Ziegler from ETH SIS)
- Microfluidic designs to study microbial interactions (with Stefano Ugolini)
- A combined microfluidics and nanoSIMS method to couple single-cell growth with metabolic activity (Glen, Benjamin, Astrid, external page Fabai Wu, external page Victoria Orphan group)
- A device to perform anaerobic microfluidics-based live-cell imaging (with external page Alyson Hockenberry, Markus Arnoldini and external page Susan Schlegel)
- The kChip, a droplet-based platform designed for the rapid, massively parallel construction and screening of synthetic microbial communities (Anna, originally developed by the external page Blainey lab)