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Introduction to Bonsai

Introduction to Bonsai

Time: TBA
Place: TBA
Number of Participants: 14
Trainer: Juan Ignacio Sanguinetti Scheck, MSc (Bernstein Center for Computational Neuroscience, Berlin)
Bonsai is an open source, visual programming software used primary for collection and analysis of behavioural data. It was created in the Champalimaud Centre for the Unknown to facilitate processing of multiple, heterogeneous data streams in real-time (Front. Neuroinform., 2015). Currently the best developed part of Bonsai is a powerful and intuitive library for video processing, allowing to track animals during experiments. The software offers also such possibilities as communication with external devices (including Arduino), adding Python scripts, and analysing multiple data streams (f.e. electrophysiological recordings). These unique features make it an ideal tool for controlling even the most sophisticated behavioral paradigms, such as closed-loop experiments.
During the workshop participants will be introduced to the Bonsai environment. They will learn in practice how to track moving objects and perform simple, on-line analysis of the collected data. Real-life mazes will be used to illustrate the principles of designing behavioural experiments. Finally, the participants will learn how Bonsai can be combined with Arduino to build custom-made behavioural equipment.

Juan Ignacio Sanguinetti Scheck (Bernstein Center for Computational Neuroscience, Berlin) has graduated from University of the Republic, Montevideo (Uruguay) has strong background in behavioural studies, including work on electric fish and mice. Currently he works as a post-doc in the lab of Michael Brecht in Bernstein Center for Computational Neuroscience, Berlin. He combines behavioural techniques with in vivo electrophysiological recordings.


Only participants who registered for the Conference are eligible to attend the workshops.

Registration for workshops will be opened in September.