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docs: add docs & how-to for datajoint pipeline #84

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2 changes: 1 addition & 1 deletion src/about/index.md
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@@ -1,7 +1,7 @@
(target-about)=
# About

The development of Aeon is funded by the [Gatsby Charitable Foundation](https://www.gatsby.org.uk/) and [Wellcome](https://wellcome.org/). This joint initiative involves people from the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/) and the [Gatsby Computational Neuroscience Unit](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit) at UCL, [NeuroGEARS Ltd](https://neurogears.org/), and [DataJoint Inc](https://www.datajoint.com/). For a full list of people involved, please refer to this [page](target-people).
The development of Aeon is funded by the [Gatsby Charitable Foundation](https://www.gatsby.org.uk/) and [Wellcome](https://wellcome.org/). This joint initiative involves people from the [Sainsbury Wellcome Centre](https://www.sainsburywellcome.org/web/) and the [Gatsby Computational Neuroscience Unit](https://www.ucl.ac.uk/gatsby/gatsby-computational-neuroscience-unit) at UCL, [NeuroGEARS Ltd](https://neurogears.org/), and [DataJoint Inc](datajoint:). For a full list of people involved, please refer to this [page](target-people).

The brain's computations are shaped by evolutionary pressures related to survival and the resulting behavioural responses.
Understanding the neural basis of natural behaviours is crucial for advancing our knowledge of the brain, as it sheds light on the functions of neural circuits in processing real-world stimuli.
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5 changes: 5 additions & 0 deletions src/conf.py
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Expand Up @@ -168,8 +168,13 @@ def get_current_release_tag():
"aeon-experiments-github": "https://github.com/SainsburyWellcomeCentre/aeon_experiments/{{path}}",
"aeon-lineardrive-github": "https://github.com/SainsburyWellcomeCentre/aeon_lineardrive/{{path}}",
"aeon-feeder-github": "https://github.com/SainsburyWellcomeCentre/aeon_feeder/{{path}}",
"datajoint": "https://datajoint.com/{{path}}",
"sample-data-single-mouse-foraging": "https://doi.org/10.5281/zenodo.13881884",
"semver": "https://semver.org/",
"sleap": "https://sleap.ai/",
"harp-tech": "https://harp-tech.org/{{path}}#{{fragment}}",
"python-pep": "https://peps.python.org/pep-{{path}}",
"niu-howto": "https://howto.neuroinformatics.dev/programming/SSH-SWC-cluster#{{fragment}}",
}

#autodoc_mock_imports = ["aeon"]
4 changes: 3 additions & 1 deletion src/getting_started/installation.md
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@@ -1,7 +1,9 @@
(target-installation)=
# Installation

This guide will walk you through the installation of the `aeon_mecha` package, the main package for interacting with raw Aeon data. It also includes instructions for setting up data access to the Aeon data hosted on SWC's Ceph storage (currently only applicable to SWC members).

(target-install-aeon-mecha)=
## `aeon_mecha`

:::{note}
Expand Down Expand Up @@ -108,4 +110,4 @@ The next step is to configure your IDE to connect to the `swc-gateway` node via
::::
:::::

Within the `aeon` conda environment, Aeon data can be accessed directly from Ceph or the DataJoint database using the [`aeon_mecha` API](target-mecha-reference). Examples for retrieving and visualizing the data can be found in the [User Guide](target-user-guide).
Within the `aeon` conda environment, Aeon data can be accessed from Ceph using the [`aeon_mecha` API](target-mecha-reference) or queried from the [Aeon DataJoint pipeline](target-aeon-dj-pipeline). Examples for retrieving and visualizing the data can be found in the [User Guide](target-user-guide).
254 changes: 254 additions & 0 deletions src/images/datajoint_analysis_diagram.svg
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