Repositories

The Aeon infrastructure is complex and multi-dimensional, spanning hardware, acquisition software, standard data formats, and a low-level API for data analysis. As each of these different components is built using different languages, including but not limited to CAD programs, Bonsai and Python, we organise Aeon into the following repositories:

aeon_acquisition

Source code for the aeon_acquisition Bonsai package used in Aeon experiment workflows.

https://github.com/SainsburyWellcomeCentre/aeon_acquisition

aeon_api

Aeon’s low-level library for interfacing with raw acquired data. Contains modules for loading and processing raw data.

https://github.com/SainsburyWellcomeCentre/aeon_api

aeon_docs

Source code for the Aeon documentation site, built via Sphinx.

https://github.com/SainsburyWellcomeCentre/aeon_docs

aeon_experiments

Aeon experiment workflows written in the Bonsai visual programming language.

https://github.com/SainsburyWellcomeCentre/aeon_experiments

aeon_feeder

Source code for pellet delivery via foraging patches used in Aeon experiments.

https://github.com/SainsburyWellcomeCentre/aeon_feeder

aeon_habitat

Contains the STEP file for the Aeon habitat and all its components.

https://github.com/SainsburyWellcomeCentre/aeon_habitat

aeon_lineardrive

Source code for actuating a linear drive motor used in Aeon experiments.

https://github.com/SainsburyWellcomeCentre/aeon_lineardrive

aeon_mecha

Aeon’s library for interfacing with the Aeon DataJoint pipeline. Contains modules for data ingestion, processing, and analysis using DataJoint.

https://github.com/SainsburyWellcomeCentre/aeon_mecha

aeon_sleap_processing

Aeon’s pose and identity tracking pipeline using SLEAP.

https://github.com/SainsburyWellcomeCentre/aeon_sleap_processing

aeon_template

Sample Aeon experiment workflow demonstrating a full acquisition pipeline.

https://github.com/SainsburyWellcomeCentre/aeon_template

Note

All experiment data is acquired and/or triggered and/or synced by Harp devices. Code in the aeon_acquisition and aeon_api repositories makes use of the Harp protocol during data acquisition, raw data file writing, and raw data file reading. See also the documentation on Harp device operation and common registers, the Harp binary protocol, and Harp clock synchronisation.