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 started with the EphysQuickstart & OphysQuickstart guides.

🔬 See the Brain Observatory Toolbox applied to neuroscience data analysis in the EphysDemo & the OphysDemo.

👩‍🏫 Learn how to use the Brain Observatory Toolbox with the EphysTutorial, OphysTutorial, & BehaviorTutorial.

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

Questions, suggestions, and other feedback are highly welcomed (in the Discussion forum).

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:

Key Concepts

• Item tables support all tabular operations, including tabular indexing which enables specific dataset item selection for inspection and analysis as item objects
• Item objects consist of numerous properties which each return direct, derived, or file-linked values about a specific item
  • Some item objects also have methods to compute values requiring additional user-specified arguments

The basic workflow is illustrated by three lines of code:

>> sessions = bot.fetchSessions('ephys')  % Obtain/view table showing available ephys session items
>> session = bot.session(sessions(1,:)) % Obtain/view object representing first available session item
>> methods(session) % Display methods (functions) available to access additional session item values

👉Try typing these three lines directly into the MATLAB command window

Technical Details

• Local caching (of retrieved item information, object representation, and file contents) is implemented, to provide the fastest possible initial and repeat performance within and across MATLAB sessions.

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

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Acknowledgements

Initial engineering work 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. ↩