Welcome
Rapid-prototyping Systems Neuroscience with Bonsai
This training course will introduce you to the basic concepts of data acquisition and behavioural control using the Bonsai visual programming language.
Course Schedule
| Monday | Tuesday | Thursday | |
|---|---|---|---|
| Morning | Introduction to Bonsai | Operant behavior | Final projects |
| Afternoon | Cameras, tracking, microcontrollers | Real-time closed-loop experiments |
Session 1 - Introduction to Bonsai
- What is visual reactive programming, and why should you care? Introduction to Bonsai.
- How to measure almost anything with Bonsai. From quantities to bytes.
- How to control almost anything with Bonsai. From bytes to effects.
- How to measure and control multiple things at the same time with one computer.
- Demos and applications: a whirlwind tour of Bonsai.
Session 2 - Cameras, tracking and microcontrollers
- Measuring behavior using video.
- Recording real-time video from multiple cameras.
- Real-time tracking of colored objects, moving objects and contrasting objects: the basic toolkit.
- Measuring behavior using voltages and an Arduino.
- A primer on data synchronization: on what frame did the light turn on?
Session 3 - Operant behavior tasks
- Modeling trial sequences: states, events, and side-effects.
- Driving state transitions with external inputs.
- Choice, timeouts and conditional logic: the basic building blocks of reaction time, Go/No-Go and 2AFC tasks.
- Combining real-time and non real-time logic for good measure.
- Student project brainstorming
Session 4 - Real-time closed-loop experimentation
- What can we learn from closed-loop experiments?
- Conditional effects. Triggering a stimulus based on video activity.
- Continuous feedback. Modulate stimulus intensity with speed or distance.
- Feedback stabilization. Record video centered around a moving object.
- Measuring closed-loop latency.
Session 5 - Final projects
- Student project presentation
- Where to next