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Reorganize software guide (#87)
* Reorganizing software guide - Add sphinx-design - Link to external pages --------- Co-authored-by: Ceci Herbert <[email protected]> Co-authored-by: Brandon Parks <[email protected]>
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‎Pipfile

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pytz = "*"
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sphinxcontrib-wavedrom = "*"
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jinja2 = "*"
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sphinx-design = "*"
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[dev-packages]

‎Pipfile.lock

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‎source/Hardware Guide/Headstages/tether-voltage.rst

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voltage can still cause connectivity issues as the headstage occasionally dips
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below the level it needs to function properly.
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.. attention:: The :ref:`Bonsai package <openephys_onix1ref>` automatically sets the
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headstage port voltage by default, but allows the user to override the
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voltage setting as well. The documentation linked shows how to use this
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functionality and what valid voltage ranges are for each headstage. This
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functionality has been been tuned for the tethers that are shipped with each
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headstage. The voltage override is available when custom tethers are used
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(see :ref:`measure_voltage`).
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.. attention::
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The `OpenEphys.Onix1 <https://open-ephys.github.io/bonsai-onix1-docs/index.html>`__
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Bonsai package automatically sets the headstage port voltage by default, but allows
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the user to override the voltage setting as well. The documentation linked shows how
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to use this functionality and what valid voltage ranges are for each headstage. This
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functionality has been been tuned for the tethers that are shipped with each
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headstage. The voltage override is available when custom tethers are used
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(see :ref:`measure_voltage`).
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The voltage set in software is not identical to the voltage supplied to the
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headstage, as some voltage drop will occur over the tether that connects them. The

‎source/Hardware Guide/Miniscopes/index.rst

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:Design Repository: https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB
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:Documentation: http://miniscope.org/index.php/Guides_and_Tutorials
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:Compatibility: :ref:`pcie_host`, :ref:`breakout`
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:Software: :ref:`openephys_onix1ref`
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:Software: `OpenEphys.Onix1 <https://open-ephys.github.io/bonsai-onix1-docs/index.html>`__ Bonsai package
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.. figure:: /_static/images/miniscopes/ucla-miniscope-v3-render.jpg
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:align: center
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:Design Repository: https://github.com/Aharoni-Lab/Miniscope-v4
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:Documentation: https://github.com/Aharoni-Lab/Miniscope-v4/wiki
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:Compatibility: :ref:`pcie_host`, :ref:`breakout`
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:Software: :ref:`openephys_onix1ref`
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:Software: `OpenEphys.Onix1 <https://open-ephys.github.io/bonsai-onix1-docs/index.html>`__ Bonsai package
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.. figure:: /_static/images/miniscopes/ucla-miniscope-v4-render.png
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:align: center

‎source/Software Guide/Bonsai.ONIX/index.rst

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.. _bonsai_onixref:
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Bonsai.ONIX
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Bonsai.ONIX (DEPRECATED)
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===================================
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..
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Important: The names of pages for nodes must match their Bonsai.ONIX class

‎source/Software Guide/Open Ephys GUI/index.rst

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.. |_| unicode:: 0xA0
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:trim:
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.. _open_ephys_gui:
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Open Ephys GUI ONIX Plugin
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Open Ephys GUI Plugin
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--------------------------------------------
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The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/index.html>`__ is an
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experiments more flexible and enjoyable. It works equally well on macOS, Linux,
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and Windows.
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.. note:: An ONIX plugin for the Open Ephys is in development. To access all of
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ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref`.
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**In the meantime, you can still take advantage of the GUI's excellent
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ephys visualizaiton tools by streaming data from Bonsai to the GUI using
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the** `Ephys Socket Plugin <https://open-ephys.github.io/gui-docs/User-Manual/Plugins/Ephys-Socket.html>`__.
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An ONIX Source plugin for the Open Ephys GUI is in development.
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To access all of ONIX's capabilities right now, have a look at the `OpenEphys.Onix1 Bonsai Package Docs <https://open-ephys.github.io/bonsai-onix1-docs/index.html>`__. Even when acquiring in Bonsai, you can still take advantage of the GUI's excellent ephys visualization tools by streaming data from Bonsai to the GUI using the Ephys Socket Plugin as explained in `this tutorial <https://open-ephys.github.io/bonsai-onix1-docs/articles/tutorials/ephys-socket.html>`__.
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‎source/Software Guide/OpenEphys.Onix1/index.rst

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‎source/Software Guide/index.rst

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.. toctree::
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:hidden:
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OpenEphys.Onix1/index
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Bonsai Package Docs <https://open-ephys.github.io/bonsai-onix1-docs/>
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Open Ephys GUI/index
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oni-repl/index
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Bonsai.ONIX (DEPRECATED) <Bonsai.ONIX/index>
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Deprecated Software<Bonsai.ONIX/index>
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:ref:`Bonsai ONIX Package <openephys_onix1ref>`
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:ref:`OpenEphys.Onix1 <openephys_onix1ref>` is a `Bonsai
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<https://bonsai-rx.org/>`__ package for acquiring data from ONIX hardware
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for real-time experiments. Bonsai is very good at processing the
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heterogeneous data streams produced by ONIX hardware.
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There are two recommended software programs to acquire data from the ONIX system:
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:ref:`Open Ephys GUI ONIX Plugin <open_ephys_gui>`
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The `Open Ephys GUI <https://open-ephys.github.io/gui-docs/>` excels at
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electrophysiology data visualization and recording.
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.. grid::
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:ref:`Command line application <oni_repl>`
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`oni-repl` is a simple command-line application that can be used for
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debugging and basic streaming IO with ONIX hardware.
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.. grid-item-card:: Bonsai Package OpenEphys.Onix1
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:link-type: url
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:link: https://open-ephys.github.io/bonsai-onix1-docs/
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:class-card: intro-card
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:img-top: /_static/images/bonsai-logo.svg
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:img-alt: bonsai logo
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:class-img-top: software-card-img
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:columns: 5
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.. tip:: ONIX uses an `ONI-compliant API
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<https://open-ephys.github.io/ONI/v1.0/api/index.html>`__ that is software
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agnostic. If you want to use ONIX hardware with your acquisition software,
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please :ref:`get in touch <support>`.
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Acquire data from ONIX in Bonsai, a visual programming language for more extensive data
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processing and sub-ms latency feedback.
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.. grid-item-card:: Open Ephys GUI Plugin ONIX Source
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:link-type: ref
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:link: open_ephys_gui
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:class-card: intro-card
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:img-top: /_static/images/oe-gui-logo.png
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:img-alt: open ephys gui logo
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:class-img-top: software-card-img
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:columns: 5
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Acquire data from ONIX in the Open Ephys GUI, a turnkey solution for acquiring and
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visualizing electrophysiology data.
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Troubleshooting & Development
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___________________________________
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:doc:`oni_repl <oni-repl/index>` is a simple command-line application that can be used for
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debugging and basic streaming IO with ONIX hardware.
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.. tip:: ONIX uses an `ONI-compliant API
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<https://open-ephys.github.io/ONI/v1.0/api/index.html>`__ that is software
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agnostic. If you want to use ONIX hardware with your acquisition software,
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please :ref:`get in touch <support>`.
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Deprecated Software
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___________________________________
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- The :ref:`bonsai_onixref` pages provide information about the original Bonsai
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package, which has been superseded by :ref:`OpenEphys.Onix1 <openephys_onix1ref>`.
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:doc:`Bonsai.ONIX <Bonsai.ONIX/index>` is the deprecated Bonsai ONIX
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package which has been superseded by `OpenEphys.Onix1 <https://open-ephys.github.io/bonsai-onix1-docs/>`__.
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‎source/_static/images/bonsai-logo.svg

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‎source/_static/images/oe-gui-logo.png

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‎source/_static/theme_overrides.css

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.hint>.admonition-title:before {
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color: #519141 !important;
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}
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.software-card-img {
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width: 50%;
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margin: auto;
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margin-top: 1rem;
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}

‎source/conf.py

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'sphinx.ext.githubpages',
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'sphinx.ext.graphviz',
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'sphinxcontrib.wavedrom',
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'sphinx_design'
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]
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# Add any paths that contain templates here, relative to this directory.

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