Update documentation

Hardware Guide/Headstages/tether-voltage.html

@@ -506,7 +506,7 @@ <h2>Setting Headstage Voltage<a class="headerlink" href="#setting-headstage-volt
 below the level it needs to function properly.</p>
 <div class="admonition attention">
 <p class="admonition-title">Attention</p>
-<p>The <a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">OpenEphys.Onix1</span></a> Bonsai package automatically sets the
+<p>The <a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">Bonsai package</span></a> 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

Hardware Guide/Miniscopes/index.html

@@ -501,7 +501,7 @@ <h2>UCLA Miniscope V3<a class="headerlink" href="#ucla-miniscope-v3" title="Link
 <dd class="field-odd"><p><a class="reference internal" href="../PCIe%20Host/index.html#pcie-host"><span class="std std-ref">PCIe Host</span></a>, <a class="reference internal" href="../Breakout%20Board/index.html#breakout"><span class="std std-ref">Breakout Board</span></a></p>
 </dd>
 <dt class="field-even">Software<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">OpenEphys.Onix1</span></a> Bonsai package</p>
+<dd class="field-even"><p><a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">Bonsai ONIX Package</span></a></p>
 </dd>
 </dl>
 <figure class="align-center">
@@ -521,7 +521,7 @@ <h2>UCLA Miniscope V4<a class="headerlink" href="#ucla-miniscope-v4" title="Link
 <dd class="field-odd"><p><a class="reference internal" href="../PCIe%20Host/index.html#pcie-host"><span class="std std-ref">PCIe Host</span></a>, <a class="reference internal" href="../Breakout%20Board/index.html#breakout"><span class="std std-ref">Breakout Board</span></a></p>
 </dd>
 <dt class="field-even">Software<span class="colon">:</span></dt>
-<dd class="field-even"><p><a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">OpenEphys.Onix1</span></a> Bonsai package</p>
+<dd class="field-even"><p><a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">Bonsai ONIX Package</span></a></p>
 </dd>
 </dl>
 <figure class="align-center">

Hardware Guide/PCIe Host/setup-windows.html

@@ -614,9 +614,7 @@ <h2>Install Device Driver<a class="headerlink" href="#install-device-driver" tit
 </section>
 <section id="install-software">
 <h2>Install Software<a class="headerlink" href="#install-software" title="Link to this heading">#</a></h2>
-<p>Have a look at the <a class="reference internal" href="../../Software%20Guide/index.html#software-guide"><span class="std std-ref"> Software Guide</span></a> page for open-source software options. We
-recommend using <a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#bonsairef"><span class="std std-ref">Bonsai</span></a> and the <a class="reference internal" href="../../Software%20Guide/OpenEphys.Onix1/index.html#openephys-onix1ref"><span class="std std-ref">OpenEphys.Onix1</span></a> Bonsai package because it provides first class
-support for all ONIX hardware features.</p>
+<p>Have a look at the <a class="reference internal" href="../../Software%20Guide/index.html#software-guide"><span class="std std-ref"> Software Guide</span></a> page for software options.</p>
 </section>
 </section>
 

Resources/faq.html

@@ -457,7 +457,7 @@
 SPI-based headstages. Have a look at <a class="reference internal" href="../Hardware%20Guide/Headstages/serialization.html#serialization"><span class="std std-ref">Coaxial Data Serialization &amp; Power</span></a> for more
 information on why.</p>
 </dd>
-<dt id="term-Why-is-there-no-Open-Ephys-GUI-plugin-for-ONIX-hardware">Why is there no Open Ephys GUI plugin for ONIX hardware?<a class="headerlink" href="#term-Why-is-there-no-Open-Ephys-GUI-plugin-for-ONIX-hardware" title="Link to this term">#</a></dt><dd><p>Have a look at the <a class="reference internal" href="../Software%20Guide/Open%20Ephys%20GUI/index.html#open-ephys-gui"><span class="std std-ref">Open Ephys GUI</span></a> page.</p>
+<dt id="term-Why-is-there-no-Open-Ephys-GUI-plugin-for-ONIX-hardware">Why is there no Open Ephys GUI plugin for ONIX hardware?<a class="headerlink" href="#term-Why-is-there-no-Open-Ephys-GUI-plugin-for-ONIX-hardware" title="Link to this term">#</a></dt><dd><p>Have a look at the <a class="reference internal" href="../Software%20Guide/Open%20Ephys%20GUI/index.html#open-ephys-gui"><span class="std std-ref">Open Ephys GUI ONIX Plugin</span></a> page.</p>
 </dd>
 <dt id="term-I-have-existing-acquisition-hardware.-Can-I-can-use-your-API-and-software-to-acquire-data-from-it">I have existing acquisition hardware. Can I can use your API and software to acquire data from it?<a class="headerlink" href="#term-I-have-existing-acquisition-hardware.-Can-I-can-use-your-API-and-software-to-acquire-data-from-it" title="Link to this term">#</a></dt><dd><p>Yes. We tried to design our API so that it decouples hardware details
 from software in a generic way. Have a look at the

Software Guide/Bonsai.ONIX/Bonsai Examples/CameraSync.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">

Software Guide/Bonsai.ONIX/Bonsai Examples/Commutator.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">

Software Guide/Bonsai.ONIX/Bonsai Examples/Headstage64.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">

Software Guide/Bonsai.ONIX/Bonsai Examples/HeadstageNP1e.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">

Software Guide/Bonsai.ONIX/Bonsai Examples/LatencyTest.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">

Software Guide/Bonsai.ONIX/Bonsai Examples/index.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="../index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">

Software Guide/Bonsai.ONIX/GettingStarted.html

@@ -365,10 +365,10 @@
      aria-label="Section Navigation">
   <p class="bd-links__title" role="heading" aria-level="1">Section Navigation</p>
   <div class="bd-toc-item navbar-nav"><ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="../OpenEphys.Onix1/index.html">Bonsai</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../Open%20Ephys%20GUI/index.html">Open Ephys GUI</a></li>
-<li class="toctree-l1 has-children"><a class="reference internal" href="../oni-repl/index.html">oni-repl</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
-<li class="toctree-l2"><a class="reference internal" href="../oni-repl/usage.html">Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../OpenEphys.Onix1/index.html">Bonsai ONIX Package</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../Open%20Ephys%20GUI/index.html">Open Ephys GUI ONIX Plugin</a></li>
+<li class="toctree-l1 has-children"><a class="reference internal" href="../oni-repl/index.html">Command Line Application</a><input class="toctree-checkbox" id="toctree-checkbox-1" name="toctree-checkbox-1" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-1"><i class="fa-solid fa-chevron-down"></i></label><ul>
+<li class="toctree-l2"><a class="reference internal" href="../oni-repl/usage.html"><code class="docutils literal notranslate"><span class="pre">oni-repl</span></code> Usage</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current active has-children"><a class="reference internal" href="index.html">Bonsai.ONIX (DEPRECATED)</a><input checked="" class="toctree-checkbox" id="toctree-checkbox-2" name="toctree-checkbox-2" type="checkbox"/><label class="toctree-toggle" for="toctree-checkbox-2"><i class="fa-solid fa-chevron-down"></i></label><ul class="current">