Brain-Observatory-Toolbox
A MATLAB toolbox for accessing and using the neural recording public datasets from the Allen Brain Observatory1.
Data releases from the Allen Brain Observatory include four datasets of neural activity recordings during presentations of visual stimuli to awake mice. Quickstart examples for each can be viewed, and readily run in MATLAB Online:
Dataset | Recordings | Experiment | Details | Quickstart Example |
---|---|---|---|---|
Visual Coding 2P 2 | 🔬 "ophys"a | Passivec | details | 👀 (view) ▶️ (run) |
Visual Coding Neuropixels 3 | ⚡ "ephys"b | Passivec | details | 👀 (view) ▶️ (run) |
Visual Behavior 2P 4 | 🔬 "ophys"a | Actived | details | 👀 (view) ▶️ (run) |
Visual Behavior Neuropixels 5 | ⚡ "ephys"b | Actived | details | (coming soon) |
a two-photon (2P) calcium imaging b large-scale neural probe recordings c presentation of various visual stimuli w/ untrained subjects d visual change detection task w/ trained subjects
Technical white papers (see Details) provide information about the experimental protocols and computational pipelines for each dataset.
These three lines of code illustrate the core workflow of the Brain Observatory Toolbox to access neural data, which is common across all datasets:
ophysSessionTable = bot.listSessions('VisualCoding', 'Ophys')
exampleSession = bot.getSessions( ophysSessionTable(1, :) )
dff = exampleSession.fluorescence_traces_dff
In the first line, listSessions
lists available items (of type Session) from the Visual Coding 2P dataset. In the second line, getSessions
creates an object to interact with the first listed item. The third line reterieves from the object fully preprocessed fluorescence traces representing the neural recording data. For further explanation, see Key Concepts and/or explore tutorials.
Demonstration examples illustrate neural data analysis concepts and practice while using the Brain Observatory Toolbox:
Dataset | Demonstration Example | About |
---|---|---|
Visual Coding 2P | 👀 (view) ▶️ (run) | TODO |
Visual Coding Neuropixels | 👀 (view) (*) | TODO |
(*) These data-intensive examples are currently recommended for use on local machines or user-configured cloud instances only, not for MATLAB Online
Tutorial examples provide step-by-step guidance for using the Brain Observatory Toolbox to access and understand the metadata, processed data, and (where applicable) raw data available in the Allen Brain Observatory datasets:
Dataset | Demonstration Example | About |
---|---|---|
Visual Coding 2P | 👀 (view) ▶️ (run) | TODO |
Visual Coding Neuropixels | 👀 (view) (*) | TODO |
(*) These data-intensive examples are currently recommended for use on local machines or user-configured cloud instances only, not for MATLAB Online
Allen Brain Observatory datasets each consist of various items of types depending on the specific dataset:
The Brain Observatory Toolbox provides a set of two functions for each dataset item type:
-
listXXX
functions return a table of available items in the dataset -
getXXX
functions return an object of selected item(s) by id(s) or table row(s)
This workflow is uniform across datasets and item types, and illustrated here:
The dataset item's contents are exposed through the object's properties and (where applicable) methods. For further guidance and explanation, see the Tutorials.
To install the Brain Observatory Toolbox persistently on a local machine or cloud instance, the Add-on Explorer is recommended:
- MATLAB (R2023b or later)
- Image Processing Toolbox (if running the Visual Coding 2P demonstration
OphysDemo.mlx
)
🚧 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.
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
-
Copyright 2016 Allen Institute for Brain Science. Allen Brain Observatory. Available from: portal.brain-map.org/explore/circuits. ↩
-
Dataset: Allen Institute MindScope Program (2016). Allen Brain Observatory -- 2-photon Visual Coding [dataset]. Available from brain-map.org/explore/circuits. Primary publication: de Vries, S. E. J., Lecoq, J. A., Buice, M. A., et al. (2020). A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex. Nature Neuroscience, 23, 138-151. https://doi.org/10.1038/s41593-019-0550-9 ↩
-
Dataset: Allen Institute MindScope Program (2019). Allen Brain Observatory -- Neuropixels Visual Coding [dataset]. Available from brain-map.org/explore/circuits. Primary publication: Siegle, J. H., Jia, X., Durand, S., et al. (2021). Survey of spiking in the mouse visual system reveals functional hierarchy. Nature, 592(7612), 86-92. https://doi.org/10.1038/s41586-020-03171-x ↩
-
Dataset: Allen Institute MindScope Program (2021). Allen Brain Observatory -- 2-photon Visual Behavior [dataset]. Available from brain-map.org/explore/circuits/visual-behavior-2p. ↩
-
Dataset: Allen Institute MindScope Program (2022). Allen Brain Observatory -- Neuropixels Visual Behavior [dataset]. ↩
引用
Ethan Meyers (2024). Brain-Observatory-Toolbox (https://github.com/MATLAB-Community-Toolboxes-at-INCF/Brain-Observatory-Toolbox/releases/tag/v0.9.4.1), GitHub. 取得済み .
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