Brain Observatory Toolbox
A MATLAB toolbox for accessing and using the neural recording public datasets from the Allen Brain Observatory1.
🚧 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:
|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.
- 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
- 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.
The easiest way to install the Brain Observatory Toolbox is to use the Add-on Explorer:
- MATLAB (R2021a)
- Image Processing Toolbox (if running the Visual Coding 2P demonstration
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.
Copyright 2019 Allen Institute for Brain Science. Visual Coding Neuropixels Dataset. Available from: portal.brain-map.org/explore/circuits/visual-coding-neuropixels. ↩
Copyright 2016 Allen Institute for Brain Science. Visual Coding 2P Dataset. Available from: portal.brain-map.org/explore/circuits/visual-coding-2p. ↩
Ethan Meyers (2023). Brain-Observatory-Toolbox (https://github.com/emeyers/Brain-Observatory-Toolbox/releases/tag/v0.9.2), GitHub. Retrieved .
MATLAB Release Compatibility
Platform CompatibilityWindows macOS Linux
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See release notes for this release on GitHub: https://github.com/emeyers/Brain-Observatory-Toolbox/releases/tag/v0.9.2
See release notes for this release on GitHub: https://github.com/emeyers/Brain-Observatory-Toolbox/releases/tag/v0.9.1