As a PhD student at ETH – EAWAG I’m working in David Jhonson’s group for filling the knowledge gap between the spatial structure and the functionality of a simple community of metabolically interacting bacteria. We are using a model system based on a denitrifying bacteria and studying their metabolic interaction under fluctuating environmental conditions. My current research is based on biostatistic and image analysis of bacterial colonies mainly using Confocal Laser Scan Microscopy (SP5 Leica) at colonies level and Wide Field microscopy at single cells level. We are developing new approaches to get more insights into the bacterial spatial metabolic interaction. For the data and image analysis I use, Phython, Matlab and FIJI.
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The web is crowded by complex, and fancy scripts, instead, I would like to share the simple and easy ones to help the beginner. I recently started to upload the very simple script to process the images. See Github: https://github.com/davideciccarese
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