Installation

This guide will walk you through the installation of the Aeon’s Python packages, aeon_api and aeon_mecha, using uv. It also includes instructions for setting up data access to the Aeon data hosted on Sainbury Wellcome Centre’s (SWC) Ceph storage (currently only applicable to SWC members).

aeon_api

PyPI

To install aeon_api from PyPI:

uv pip install swc-aeon

Source

To install aeon_api from source, first clone the repository and switch to the aeon_api directory:

git clone https://github.com/SainsburyWellcomeCentre/aeon_api
cd aeon_api

(Optional) To select a specific branch, replace branch_name with the desired branch name:

git checkout branch_name

To install the package alongside all optional dependencies:

uv sync --all-extras

If you wish to install only the core dependencies, simply drop the --all-extras flag from the command above.

aeon_mecha

As aeon_mecha depends on aeon_api, installing aeon_mecha will also install aeon_api and its dependencies. In other words, you only need to install aeon_mecha to access both packages.

To install aeon_mecha, first clone the repository and switch to the aeon_mecha directory:

git clone https://github.com/SainsburyWellcomeCentre/aeon_mecha
cd aeon_mecha

(Optional) To select a specific branch, replace branch_name with the desired branch name:

git checkout branch_name

To install the package alongside all optional dependencies:

uv sync --all-extras

If you wish to install only the core dependencies, simply drop the --all-extras flag from the command above.

SWC Ceph data access

Important

You must be an SWC aeon project member to access Aeon data hosted on SWC’s Ceph storage. The required sets of credentials are as follows:

• Microsoft Teams: contact Jai Bhagat, Gonçalo Lopes, or Dario Campagner

• SWC Github organization: contact SWC Helpdesk

• SWC Github aeon project: contact Jai Bhagat or Gonçalo Lopes

• SWC HPC: contact SWC Helpdesk

• aeon HPC Linux group: contact SWC Helpdesk

• Datajoint database username: contact Thinh Nguyen

To be granted these credentials, please send a single email to all contact parties requesting this access.

Local

Note

The links below point to the SWC internal wiki, which is only accessible from within the SWC network (or using VPN).

In order to access Aeon data locally, you need to be on the SWC network or connected via VPN. You also need to mount the Ceph storage on your local machine. The Ceph storage path for different operating systems can be found here, replacing xxxxxxxx with aeon.

Remote

For using an IDE (e.g. VS Code, PyCharm Professional, Jupyter, etc.) to access Aeon data, you will need to configure the connection to SWC’s HPC using SSH. Please ensure you have met all the prerequisites before proceeding. In order to avoid typing the SSH commands each time you log into the HPC, we recommend modifying the SSH config file following this guide. The next step is to configure your IDE to connect to the swc-gateway node via SSH. These instructions can typically be found in your IDE’s online documentation. Here are the instructions for VS Code, and for PyCharm Professional.

Raw Aeon data can be accessed using aeon_api, whereas processed data can be queried from the Aeon DataJoint pipeline using aeon_mecha. Examples for retrieving and visualising the data can be found in the User Guide.