Welcome

Welcome to CF.Bonsai, a website from the Champalimaud Foundation that contains annotated examples of recurring neuroscience tasks programmed in Bonsai. Many of these examples make use of the Harp hardware protocol to interface with a variety of peripheral devices.

Getting started

Start by installing the necessary Bonsai and Harp software from the Getting Started menu on the left panel. Then, find your example of choice, and follow the instructions to run it. Every example can be copied directly to Bonsai, and includes a set of annotations that explain the most significant parts of the code. If the example involves hardware (as those of Harp) additional electrical diagrams are provided with the necessary connections between the components.

Contributions

You can place suggestions for new examples, or report any issues concerning the existing examples here. If you want to contribute with your own examples please follow the guidelines described in the cf.bonsai repository. For issues concerning Bonsai, please use the official channels.

Bonsai

Bonsai is an open-source visual language for reactive programming. It is lightweight and easy to use with a variety of packages and modules for interfacing with hardware and for real-time processing and manipulation of data streams.

More information about Harp can be found at bonsai-rx.org.

Harp

Harp is an open-source standard for asynchronous real-time data acquisition and experimental control in neuroscience. The Harp ecosystem currently includes devices to configure, control and collect data from a wide range of peripheral devices such as cameras, LEDs, nosepokes and motors.

More information about Harp can be found at harp-tech.org.