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

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6d0f747
docs: add docs & how-to for datajoint pipeline
ttngu207 Dec 5, 2024
3393ba8
Suggestions for DJ pipeline tutorial
lochhh Dec 10, 2024
0efad44
Add images and make them clickable
lochhh Dec 10, 2024
ac4ace4
Move DJ guides into User Guide
lochhh Dec 10, 2024
1f1e10e
feat(dj-docs): extend `how-to` notebook with a mini section on data q…
ttngu207 Dec 12, 2024
32a322d
Show only page titles in User Guide TOC
lochhh Dec 16, 2024
59a984f
Suggestions for DJ pipeline local deployment guide
lochhh Dec 16, 2024
0064499
Add "see also" to DJ pipeline tutorial
lochhh Dec 16, 2024
c298496
Prefix DataJoint docs/guides with `dj_`
lochhh Dec 16, 2024
b213a0a
Move data query into another notebook
lochhh Dec 17, 2024
a44fbb6
Use explicit targets
lochhh Dec 17, 2024
7d14236
Clarify `ceph_aeon` config example
lochhh Dec 17, 2024
564dc3a
Mention DJ pipeline in installation
lochhh Dec 17, 2024
c50d204
Rename image dir
lochhh Dec 18, 2024
be58bde
Update `ceph_aeon` example
lochhh Dec 18, 2024
c0bd22f
Fix import in data ingestion notebook
lochhh Dec 19, 2024
65a1ed4
docs: update notebook by enhancing descriptions and adding cell outputs
MilagrosMarin Feb 5, 2025
ee33138
docs: update `dj_querying_data` notebook
MilagrosMarin Feb 6, 2025
4f086d6
Add glossary terms
lochhh Feb 25, 2025
b3da7be
Add references to glossary
lochhh Feb 25, 2025
ba5235d
Update references
lochhh Feb 25, 2025
42bfa58
Update `dj_querying_data` notebook
lochhh Feb 25, 2025
c876092
chore: remove `create_socialexperiment_0.py`
ttngu207 Mar 4, 2025
720c92d
chore: add a step to manually created one block of interest
ttngu207 Mar 4, 2025
c332a5e
Combine insert block and subjects step in dj_data_ingestion notebook
lochhh Mar 5, 2025
275e573
Simplify MySQL setup instructions
lochhh Mar 6, 2025
64cd5b5
Execute code in dj_data_ingestion notebook
lochhh Mar 6, 2025
997df5b
Update `dj_querying_data` notebook output
lochhh Mar 6, 2025
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2 changes: 1 addition & 1 deletion src/about/index.md
Original file line number Diff line number Diff line change
@@ -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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3 changes: 3 additions & 0 deletions src/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -175,8 +175,11 @@ 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",
"myst-parser": "https://myst-parser.readthedocs.io/en/latest/{{path}}#{{fragment}}",
"semver": "https://semver.org/",
"sleap": "https://sleap.ai/{{path}}#{{fragment}}",
"harp-tech": "https://harp-tech.org/{{path}}#{{fragment}}",
"python-pep": "https://peps.python.org/pep-{{path}}",
"sphinx-doc": "https://www.sphinx-doc.org/en/master/usage/{{path}}#{{fragment}}",
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4 changes: 3 additions & 1 deletion src/getting_started/installation.md
Original file line number Diff line number Diff line change
@@ -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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