Brain-Observatory-Toolbox

A MATLAB toolbox for interacting with the Allen Brain Observatory

Brain Observatory Toolbox

A MATLAB toolbox for accessing and using the neural recording public datasets from the Allen Brain Observatory¹.

🗺️ Get oriented and get started with 3 lines of code. You can:

• Open in MATLAB Online
• Enter >>bot.README on your own local/cloud installation

Either will orient you to several live script examples available to guide new users, including demos of neural data analysis & tutorials covering Brain Observatory Toolbox concepts & operations.

You can also individually view (👀) or run (▶️) these examples on MATLAB Online:

Example Type	Data Type	View	Run	Data Type	View	Run
🚀 Quickstart	Calcium Imaging (Ophys)	👀	▶️	Neuropixels Probe (Ephys)	👀	▶️
🔬 Demo	Calcium Imaging (Ophys)	👀	▶️	Neuropixels Probe (Ephys)	👀	(*)
👩‍🏫 Tutorial	Calcium Imaging (Ophys)	👀	▶️	Neuropixels Probe (Ephys)	👀	(*)

_{(*) These data-intensive examples are currently recommended for use on local machines or customer cloud instances only, not for MATLAB Online}

🚧 The Brain Observatory Toolbox is at an early stage; the interface is not guaranteed stable across the v0.9.x releases.

💬 Questions? Suggestions? Roadblocks? Code contributors are regularly monitoring user-posted GitHub issues & the File Exchange discussion.

About the Allen Brain Observatory datasets

Data releases from the Allen Brain Observatory include two datasets of neural activity recordings:

Dataset	Recording Type	Nickname	Details
Visual Coding Neuropixels 2	Large-scale neural probe recordings	"ephys" (electrophysiology)	details
Visual Coding 2P 3	Two-photon calcium imaging	"ophys" (optical physiology)	details

The Visual Coding datasets are both collected from the living mouse brain during presentation of varying visual stimuli. Technical white papers (see Details for each dataset) provide detailed information about the experimental technicalities and computational pipelines.

About the Brain Observatory Toolbox (BOT)

The Brain Observatory Toolbox (BOT) provides a uniform interface to access and use the Visual Coding neural datasets.

The BOT interface provides tabular representations of available dataset items and object representations of specific dataset items:

Installation

The easiest way to install the Brain Observatory Toolbox is to use the Add-on Explorer:

1. Launch the Add-on Explorer
2. Search for "Brain Observatory Toolbox"
3. Press the "Add" button.

Required products

• MATLAB (R2021a or later)
• Image Processing Toolbox (if running the Visual Coding 2P demonstration OphysDemo.mlx)

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Acknowledgements

Initial engineering work, done by Ethan Meyers and Xinzhu Fang, was supported by the Foundation of Psychocultural Research and Sherman Fairchild Award at Hampshire College and hosted by the Center for Brains, Minds, and Machines at the Massachusetts Institute of Technology.

Footnotes

1. Copyright 2016 Allen Institute for Brain Science. Allen Brain Observatory. Available from: portal.brain-map.org/explore/circuits. ↩

2. Copyright 2019 Allen Institute for Brain Science. Visual Coding Neuropixels Dataset. Available from: portal.brain-map.org/explore/circuits/visual-coding-neuropixels. ↩

3. Copyright 2016 Allen Institute for Brain Science. Visual Coding 2P Dataset. Available from: portal.brain-map.org/explore/circuits/visual-coding-2p. ↩