Quentin Geissmann

Developer webpage

(Under Construction)

About me

I am a biologist interested in data analysis and programming. I work at the University of Sheffield and the Free University of Berlin. I use programming (mainly C++ and R) to help answering biological questions. Feel free to contact me.

My Projects


OpenCFU OpenCFU is a program dedicated to the counting of bacterial colonies from digital images or video devices. It is developed in C++ using OpenCV for image processing and Gtkmm for the GUI. This work has recently been published in PLoS ONE.


Ubitrail Ubitrail is an ongoing project aimed at providing a tool to record positional data of animals from videos. It implements a versatile algorithm that effectively learns the appearance of the tracked animal. It is therefore easy to track very different animals without having to change any parameters. The project also provides a simple R package, Rubitrail, that allows users to read and process data from Ubitrail.

Open Source for an Open Science

I am also involved in the free and open source software movement. I believe this is extremely important for the future of scientific research which increasingly relies on computer software. In fact, most of the time, the results presented in contemporary scientific papers have been, to some degree, generated or transformed by a computer program. Therefore, if we want science to be peer-reviewed and open, everyone should be able to "read" the programs and, if we want a science in which we build on top of others' work, scientists should be able to modify and redistribute programs made by other researchers. There are some very interesting opinions about this here and there.

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