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"hashes": [ @@ -701,6 +767,13 @@ "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923" ], "version": "==0.5.1" + }, + "xcffib": { + "hashes": [ + "sha256:33775c1d0461f19255fc54e22ce914e10a13fb65bc7bba0eabafee7f0878cfdb" + ], + "markers": "python_version >= '3.3'", + "version": "==1.7.1" } }, "develop": {} diff --git a/source/Hardware Guide/Headstages/tether-voltage.rst b/source/Hardware Guide/Headstages/tether-voltage.rst index 1814dd2..cdee0a4 100644 --- a/source/Hardware Guide/Headstages/tether-voltage.rst +++ b/source/Hardware Guide/Headstages/tether-voltage.rst @@ -20,13 +20,14 @@ host computer will not be able to detect the headstage. A borderline voltage can still cause connectivity issues as the headstage occasionally dips below the level it needs to function properly. -.. attention:: The :ref:`Bonsai package ` automatically sets the - headstage port voltage by default, but allows the user to override the - voltage setting as well. The documentation linked shows how to use this - functionality and what valid voltage ranges are for each headstage. This - functionality has been been tuned for the tethers that are shipped with each - headstage. The voltage override is available when custom tethers are used - (see :ref:`measure_voltage`). +.. attention:: + The `OpenEphys.Onix1 `__ + Bonsai package automatically sets the headstage port voltage by default, but allows + the user to override the voltage setting as well. The documentation linked shows how + to use this functionality and what valid voltage ranges are for each headstage. This + functionality has been been tuned for the tethers that are shipped with each + headstage. The voltage override is available when custom tethers are used + (see :ref:`measure_voltage`). The voltage set in software is not identical to the voltage supplied to the headstage, as some voltage drop will occur over the tether that connects them. The diff --git a/source/Hardware Guide/Miniscopes/index.rst b/source/Hardware Guide/Miniscopes/index.rst index 92d479b..94262ec 100644 --- a/source/Hardware Guide/Miniscopes/index.rst +++ b/source/Hardware Guide/Miniscopes/index.rst @@ -10,7 +10,7 @@ UCLA Miniscope V3 :Design Repository: https://github.com/daharoni/Miniscope_CMOS_Imaging_Sensor_PCB :Documentation: http://miniscope.org/index.php/Guides_and_Tutorials :Compatibility: :ref:`pcie_host`, :ref:`breakout` -:Software: :ref:`openephys_onix1ref` +:Software: `OpenEphys.Onix1 `__ Bonsai package .. figure:: /_static/images/miniscopes/ucla-miniscope-v3-render.jpg :align: center @@ -21,7 +21,7 @@ UCLA Miniscope V4 :Design Repository: https://github.com/Aharoni-Lab/Miniscope-v4 :Documentation: https://github.com/Aharoni-Lab/Miniscope-v4/wiki :Compatibility: :ref:`pcie_host`, :ref:`breakout` -:Software: :ref:`openephys_onix1ref` +:Software: `OpenEphys.Onix1 `__ Bonsai package .. figure:: /_static/images/miniscopes/ucla-miniscope-v4-render.png :align: center diff --git a/source/Software Guide/Bonsai.ONIX/index.rst b/source/Software Guide/Bonsai.ONIX/index.rst index 5f6ed69..52cd86d 100644 --- a/source/Software Guide/Bonsai.ONIX/index.rst +++ b/source/Software Guide/Bonsai.ONIX/index.rst @@ -7,7 +7,7 @@ .. _bonsai_onixref: -Bonsai.ONIX +Bonsai.ONIX (DEPRECATED) =================================== .. Important: The names of pages for nodes must match their Bonsai.ONIX class diff --git a/source/Software Guide/Open Ephys GUI/index.rst b/source/Software Guide/Open Ephys GUI/index.rst index b927d14..e60b6ad 100644 --- a/source/Software Guide/Open Ephys GUI/index.rst +++ b/source/Software Guide/Open Ephys GUI/index.rst @@ -1,6 +1,9 @@ +.. |_| unicode:: 0xA0 + :trim: + .. _open_ephys_gui: -Open Ephys GUI ONIX Plugin +Open Ephys GUI Plugin -------------------------------------------- The `Open Ephys GUI `__ is an @@ -9,11 +12,8 @@ electrophysiology data. It was designed by neuroscientists to make their experiments more flexible and enjoyable. It works equally well on macOS, Linux, and Windows. -.. note:: An ONIX plugin for the Open Ephys is in development. To access all of - ONIX's capabilities right now, have a look at the :ref:`openephys_onix1ref`. - **In the meantime, you can still take advantage of the GUI's excellent - ephys visualizaiton tools by streaming data from Bonsai to the GUI using - the** `Ephys Socket Plugin `__. +An ONIX Source plugin for the Open Ephys GUI is in development. +To access all of ONIX's capabilities right now, have a look at the `OpenEphys.Onix1 Bonsai Package Docs `__. 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 `__. diff --git a/source/Software Guide/OpenEphys.Onix1/index.rst b/source/Software Guide/OpenEphys.Onix1/index.rst deleted file mode 100644 index fc3374f..0000000 --- a/source/Software Guide/OpenEphys.Onix1/index.rst +++ /dev/null @@ -1,46 +0,0 @@ -.. _openephys_onix1ref: - -Bonsai ONIX Package -================================= - -``OpenEphys.Onix1`` is a `Bonsai `__ package for ONIX -hardware. This package contains `Bonsai Operators -`__ for acquiring and -sending data to ONIX hardware. - -:Code: https://github.com/open-ephys/bonsai-onix1 -:Compatibility: All ONIX hardware, Neuropixels, UCLA miniscopes & variants -:Documentation: https://open-ephys.github.io/bonsai-onix1-docs/index.html - -.. raw:: html - - -
- -
-

Go to the OpenEphys.Onix1 Docs

-
- OpenEphys.Onix1 bonsai
-            package documentation - -
- -What is Bonsai? ------------------------------- -`Bonsai `__ is a visual programming language (think -LabView) for `reactive programming -`__ with features such as: - -- Real-time compilation of workflows to machine code as they are edited - (zero-overhead). -- A large array of operators for combining and sychronizing asynchronous data - streams, which is a major issue in other software. -- Lots of support for all sorts of hardware outside of ONIX. - -Bonsai is A good choice for accessing the full power of ONIX hardware and -combining it with third-party data sources (e.g. machine vision cameras, -behavioral hardware, etc.), and for real-time processing and manipulation of -data streams. The documentation linked above contains detailed instructions on -how to use Bonsai with ONIX hardware along with fully useable example workflows, -data loading scripts, etc. diff --git a/source/Software Guide/index.rst b/source/Software Guide/index.rst index 62e1f80..fe112bd 100644 --- a/source/Software Guide/index.rst +++ b/source/Software Guide/index.rst @@ -9,33 +9,54 @@ .. toctree:: :hidden: - OpenEphys.Onix1/index + Bonsai Package Docs Open Ephys GUI/index oni-repl/index - Bonsai.ONIX (DEPRECATED) + Deprecated Software -:ref:`Bonsai ONIX Package ` - :ref:`OpenEphys.Onix1 ` is a `Bonsai - `__ package for acquiring data from ONIX hardware - for real-time experiments. Bonsai is very good at processing the - heterogeneous data streams produced by ONIX hardware. +There are two recommended software programs to acquire data from the ONIX system: -:ref:`Open Ephys GUI ONIX Plugin ` - The `Open Ephys GUI ` excels at - electrophysiology data visualization and recording. +.. grid:: -:ref:`Command line application ` - `oni-repl` is a simple command-line application that can be used for - debugging and basic streaming IO with ONIX hardware. + .. grid-item-card:: Bonsai Package OpenEphys.Onix1 + :link-type: url + :link: https://open-ephys.github.io/bonsai-onix1-docs/ + :class-card: intro-card + :img-top: /_static/images/bonsai-logo.svg + :img-alt: bonsai logo + :class-img-top: software-card-img + :columns: 5 -.. tip:: ONIX uses an `ONI-compliant API - `__ that is software - agnostic. If you want to use ONIX hardware with your acquisition software, - please :ref:`get in touch `. + Acquire data from ONIX in Bonsai, a visual programming language for more extensive data + processing and sub-ms latency feedback. + + .. grid-item-card:: Open Ephys GUI Plugin ONIX Source + :link-type: ref + :link: open_ephys_gui + :class-card: intro-card + :img-top: /_static/images/oe-gui-logo.png + :img-alt: open ephys gui logo + :class-img-top: software-card-img + :columns: 5 + + Acquire data from ONIX in the Open Ephys GUI, a turnkey solution for acquiring and + visualizing electrophysiology data. + + +Troubleshooting & Development +___________________________________ + +:doc:`oni_repl ` is a simple command-line application that can be used for +debugging and basic streaming IO with ONIX hardware. + +.. tip:: ONIX uses an `ONI-compliant API + `__ that is software + agnostic. If you want to use ONIX hardware with your acquisition software, + please :ref:`get in touch `. Deprecated Software ___________________________________ -- The :ref:`bonsai_onixref` pages provide information about the original Bonsai - package, which has been superseded by :ref:`OpenEphys.Onix1 `. +:doc:`Bonsai.ONIX ` is the deprecated Bonsai ONIX +package which has been superseded by `OpenEphys.Onix1 `__. diff --git a/source/_static/images/bonsai-logo.svg b/source/_static/images/bonsai-logo.svg new file mode 100644 index 0000000..fd5144b --- /dev/null +++ b/source/_static/images/bonsai-logo.svg @@ -0,0 +1,98 @@ + + + + + + + + + + + + + image/svg+xml + + + + + + + + + + + diff --git a/source/_static/images/oe-gui-logo.png b/source/_static/images/oe-gui-logo.png new file mode 100644 index 0000000..55e918f Binary files /dev/null and b/source/_static/images/oe-gui-logo.png differ diff --git a/source/_static/theme_overrides.css b/source/_static/theme_overrides.css index c30c417..6947161 100644 --- a/source/_static/theme_overrides.css +++ b/source/_static/theme_overrides.css @@ -436,3 +436,9 @@ img { .hint>.admonition-title:before { color: #519141 !important; } + +.software-card-img { + width: 50%; + margin: auto; + margin-top: 1rem; +} \ No newline at end of file diff --git a/source/conf.py b/source/conf.py index f9d9e71..ba131f6 100644 --- a/source/conf.py +++ b/source/conf.py @@ -43,6 +43,7 @@ 'sphinx.ext.githubpages', 'sphinx.ext.graphviz', 'sphinxcontrib.wavedrom', + 'sphinx_design' ] # Add any paths that contain templates here, relative to this directory.