Introduction to Bonsai

Bonsai

Introduction to Bonsai

neurogears.org/neuroinformatics-2024

Outline

What is Bonsai?
Hardware & Software Ecosystem
- Harp
- Open-Ephys
- Fiber photometry, etc
- DeepLabCut, SLEAP
- ...

What is Bonsai?

Reactive Programming

What is Bonsai?

Reactive Programming

What is Bonsai?

Reactive Programming

What is Bonsai?

Bonsai

Why do we need a new algebra?

Behavior Experiments

Why do we need a new algebra?

Behavior Experiments

Why do we need a new algebra?

Behavior Experiments

Why do we need a new algebra?

Behavior Experiments

Why do we need a new algebra?

Behavior Experiments

Why do we need a new algebra?

Behavior Experiments

Workflow Marble diagram

Workflow Marble diagram

Workflow Marble diagram

Workflow Marble diagram

Workflow Marble diagram

Workflow Marble diagram

Workflow Marble diagram

Bonsai workflow editor

Bonsai Ecosystem

Gonçalo Lopes, Kampff Lab

Lorenza Calcaterra, Kampff Lab

Joana Neto et al., Kampff Lab

George Dimitriadis, Kampff Lab

Hardware synchronized acquisition & control

Harp-Bonsai

Next generation open ephys

ONI - Open Neuro Interface

open-ephys.github.io/onix-docs

Jon Newman et al. @ Open-Ephys

Multi-fiber photometry recordings

Neurophotometrics

Neurophotometrics

neurophotometrics.com

Interactive visual environments

BonVision

Augmented Reality in BonVision

bonvision.github.io

Saleem Lab and Solomon Lab

Real-time markerless pose estimation

Bonsai-DeepLabCut

github.com/bonsai-rx/deeplabcut

Mathis et al., Nat Neurosci, 2018

Multi-animal tracking

BonZeb

ncguilbeault.github.io/BonZeb

Guilbeault et al., Sci Rep, 2021

Multi-animal pose and identity tracking

Bonsai-SLEAP

bonsai-rx.org/sleap

Pereira et al., Nat Methods, 2022

Bonsai

Questions?

neurogears.org/neuroinformatics-2024

Introduction to Bonsai neurogears.org/neuroinformatics-2024