Introduction to Bonsai

Introduction to Bonsai

Time: 24th November, 12 am - 5:45 pm
Place: Nencki Institute of Experimental Biology
Number of Participants: 14
Trainer: Juan Ignacio Sanguinetti Scheck, MSc (Bernstein Center for Computational Neuroscience, Berlin) and Gonçalo Lopes, MSc (Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal)
 
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Note: Only participants who registered for the Conference are eligible to attend the workshops.
 
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.
Gonçalo Lopes (Champalimaud Foundation, Centre for the Unknown, Lisbon, Portugal) is fascinated by intelligent systems and started out his research in 2006 developing interactive real-time systems at the YLabs, the R&D division of YDreams. There he became one of the lead architects behind the YVision software framework and conducted applied research in augmented reality, computer vision, parallel processing and autonomous agents.
In 2010, hoping to find better ways of building machines that learn by themselves, he decided to study Neuroscience as a way to take inspiration from systems that can already solve these kinds of problems: brains. He joined the Champalimaud Neuroscience PhD Programme where he worked with Adam Kampff and Joe Paton to understand a robust role for motor cortex in the control of movement.
Along the way, Gonçalo extended his experience making interactive systems to rodents and other animal models. He started developing Bonsai as a way to rapidly prototype behaviour experiments and all kinds of experimental neuroscience rigs.
 

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