aeon_mecha

Project Aeon's main repository for manipulating acquired data. Includes modules for loading raw data, performing quality control on raw data, processing raw data, and ingesting processed data into a DataJoint MySQL database.

Set-up Instructions

Remote set-up on SWC's HPC

1. SSH into the HPC and clone this repository:

ssh <your_SWC_username>@ssh.swc.ucl.ac.uk
mkdir ~/ProjectAeon && cd ~/ProjectAeon
git clone https://github.com/SainsburyWellcomeCentre/aeon_mecha
cd aeon_mecha

2. Follow the remote set-up instructions.

Local set-up

Run commands in a bash shell. Windows users can use the 'mingw64' terminal included with git.

1. Clone this repository:

mkdir ~/ProjectAeon && cd ~/ProjectAeon
git clone https://github.com/SainsburyWellcomeCentre/aeon_mecha
cd aeon_mecha

2. Follow the local set-up instructions.

Repository Contents

• .github/workflows/ : GitHub actions workflows for building the environment and running tests
• aeon/ : Source code for the Aeon Python package
  • aeon/dj_pipeline: Source code for the Aeon DataJoint MySQL database pipeline
  • aeon/io: Source code for loading raw data
  • aeon/processing: Source code for processing raw data
  • aeon/qc: Source code for quality control of raw data
  • aeon/schema: Examples of 'experiment schemas': variables that can be used to load raw data from particular experiments
• docker/ : Dockerfiles for building Docker images for the Aeon DataJoint MySQL database pipeline.
• docs/ : Documentation for the Aeon project
  • docs/devs/ : Documentation for developers
  • docs/env_setup/ : Documentation for setting up the Aeon Python environment
  • docs/examples/ : Aeon usecase examples
  • docs/using_hpc_jupyterhub.md : Instructions for using Jupyter notebooks to access Aeon data via SWC's HPC
  • docs/using_online_dashboard.md : Instructions for connecting to Aeon's online dashboard
• env_config/ : Configuration files for the Aeon Python environment
• tests/ : Unit and integration tests
  • tests/data : Data used by tests

Citation Policy

If you use this software, please cite it as below:

D. Campagner, J. Bhagat, G. Lopes, L. Calcaterra, A. G. Pouget, A. Almeida, T. T. Nguyen, C. H. Lo, T. Ryan, B. Cruz, F. J. Carvalho, Z. Li, A. Erskine, J. Rapela, O. Folsz, M. Marin, J. Ahn, S. Nierwetberg, S. C. Lenzi, J. D. S. Reggiani, SGEN group – SWC GCNU Experimental Neuroethology Group. Aeon: an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales. Preprint at https://doi.org/10.1101/2025.07.31.664513 (2025)