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18 changes: 6 additions & 12 deletions Getting Started/index.html
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<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
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<p>Read <a class="reference internal" href="warnings.html#warnings"><span class="std std-ref">Usage Warnings</span></a> before starting to work with the system to avoid causing damage to system components.</p>
</div>
</section>
<section id="setting-up-onix">
<h2>Setting up ONIX<a class="headerlink" href="#setting-up-onix" title="Link to this heading">#</a></h2>
<section id="setting-up-your-system">
<h2>Setting up your system<a class="headerlink" href="#setting-up-your-system" title="Link to this heading">#</a></h2>
<ol class="arabic">
<li><p>Check that you have all the necessary hardware. A full ONIX setup consists of:</p>
<p><strong>Hardware</strong></p>
Expand Down Expand Up @@ -484,18 +484,12 @@ <h2>Setting up ONIX<a class="headerlink" href="#setting-up-onix" title="Link to
<a class="reference internal" href="../Hardware%20Guide/Headstages/setup.html#headstage-setup"><span class="std std-ref">following these steps</span></a>. Be sure to read <a class="reference internal" href="../Hardware%20Guide/Headstages/tether-voltage.html#tether-voltage"><span class="std std-ref">this
page on the voltage supplied to the headstage</span></a> to prevent
damaging your headstage.</p></li>
<li><p>Test the installation.</p>
<div class="admonition-todo admonition" id="id2">
<p class="admonition-title">Todo</p>
<p>Bonsai workflows for testing each component</p>
</div>
</li>
</ol>
</section>
<section id="using-onix">
<h2>Using ONIX<a class="headerlink" href="#using-onix" title="Link to this heading">#</a></h2>
<p>ONIX uses Bonsai for data acquisition. See the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/GettingStarted.html#bonsai-gettingstarted"><span class="std std-ref">Getting Started</span></a>
page to learn how to install Bonsai and use it to acquire from ONIX.</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 to explore
software options and for intefacing with ONIX hardware.</p>
</section>
</section>

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<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#understanding-the-system">Understanding the System</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#usage-warnings">Usage Warnings</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#setting-up-onix">Setting up ONIX</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#setting-up-your-system">Setting up your system</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#using-onix">Using ONIX</a></li>
</ul>
</nav></div>
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2 changes: 1 addition & 1 deletion Getting Started/troubleshooting.html
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105 changes: 21 additions & 84 deletions Getting Started/warnings.html
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Expand Down Expand Up @@ -431,96 +431,33 @@ <h1>Usage Warnings<a class="headerlink" href="#usage-warnings" title="Link to th
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Improper setup and usage can cause damage to system components.</p>
</div>
<ul class="simple">
<li><p>Read the following warnings before starting to work with your system. These are crucial
aspects to consider during setup and usage that are included in the documentation but
are listed here for your convenience.</p></li>
<li><p>Read the complete documentation carefully to understand how the system works and refer
back to these warnings before using it.</p></li>
</ul>
<section id="hardware">
<h2>Hardware<a class="headerlink" href="#hardware" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p>Connecting or disconnecting the breakout board while the PC is on causes damage to the
FMChost. For more details, see <a class="reference internal" href="../Hardware%20Guide/Breakout%20Board/setup.html#breakout-setup"><span class="std std-ref">Breakout Board Guide</span></a>.</p></li>
<li><p>Read the following warnings before starting to work with your system. These
are crucial aspects to consider during setup and usage that are included in
the documentation but are listed here for your convenience.</p></li>
<li><p>Read the complete documentation carefully to understand how the system works
and refer back to these warnings before using it.</p></li>
</ul>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p><strong>Power off the PC before connecting/disconnecting the breakout board.</strong></p>
</div>
<ul class="simple">
<li><p>Headstage voltage must be configured correctly for operation. The voltage that works
for one headstage can damage another, and depends on your hardware configuration such
as tether length. For more details, see <a class="reference internal" href="../Hardware%20Guide/Headstages/tether-voltage.html#tether-voltage"><span class="std std-ref">Tethered Headstage Voltages</span></a>.</p></li>
</ul>
<section id="breakout-board">
<h2>Breakout Board<a class="headerlink" href="#breakout-board" title="Link to this heading">#</a></h2>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p><strong>Ensure each headstage is configured with the correct voltage according to its
specification before connecting and switching on the headstage port switch.</strong></p>
<p>Connecting or disconnecting the <a class="reference internal" href="../Hardware%20Guide/Breakout%20Board/index.html#breakout"><span class="std std-ref">Breakout Board</span></a> while the PC is on
can damage to the <a class="reference internal" href="../Hardware%20Guide/PCIe%20Host/index.html#pcie-host"><span class="std std-ref">PCIe Host</span></a>. For more details, see
<a class="reference internal" href="../Hardware%20Guide/Breakout%20Board/setup.html#breakout-setup"><span class="std std-ref">Breakout Board Guide</span></a>. <strong>Power off the PC before connecting/disconnecting the
breakout board.</strong></p>
</div>
</section>
<section id="software">
<h2>Software<a class="headerlink" href="#software" title="Link to this heading">#</a></h2>
<p><em>For the current Bonsai.ONIX library which is being revised to improve usability</em></p>
<ul class="simple">
<li><p>Headstage port voltage configuration is managed via the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/ONIContext.html#bonsai-onicontext"><span class="std std-ref">ONIContext</span></a> node
or the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/HeadstagePortControlDevice.html#bonsai-headstageportcontroldev"><span class="std std-ref">HeadstagePortControlDevice</span></a> node. The changes you make using these
nodes apply immediately and persist in hardware even if the Bonsai workflow is not
running. Headstage port voltage is reset to the default 4.9V only on a power cycle
(power off and on — not reboot).</p></li>
</ul>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p><strong>Keep the headstage port switches off until you have configured each port correctly.</strong></p>
</div>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p><strong>Remember to set the headstage voltage to the desired value after a power cycle.</strong></p>
</div>
<ul class="simple">
<li><p>The <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/ONIContext.html#bonsai-onicontext"><span class="std std-ref">ONIContext</span></a> provides a dynamic window to read and write to hardware,
but parameters such as device voltage are not saved in the node when the workflow is
saved. The <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/HeadstagePortControlDevice.html#bonsai-headstageportcontroldev"><span class="std std-ref">HeadstagePortControlDevice</span></a> node also reads and writes to hardware,
but parameters are saved with the workflow. On loading a workflow, Bonsai writes the
parameter values set when the workflow was last saved.</p></li>
</ul>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>When you configure the voltage, the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/ONIContext.html#bonsai-onicontext"><span class="std std-ref">ONIContext</span></a> node shows that value
and when you save the workflow this value is not saved. Therefore, that value will
not be set to hardware when you load the workflow again. On loading the workflow,
the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/ONIContext.html#bonsai-onicontext"><span class="std std-ref">ONIContext</span></a> node will be reading the voltage that is already set
on the hardware and showing this in the <code class="docutils literal notranslate"><span class="pre">LinkVoltage</span></code> field.</p>
</div>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>When you configure the voltage, the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/HeadstagePortControlDevice.html#bonsai-headstageportcontroldev"><span class="std std-ref">HeadstagePortControlDevice</span></a> node shows
that value and when you save the workflow this value is saved. Therefore, that value
will be set to hardware when you load the workflow again. If you make changes to the
voltage value (with any node) and save the workflow, they will be saved in the
<code class="docutils literal notranslate"><span class="pre">LinkVoltage</span></code> property of the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/HeadstagePortControlDevice.html#bonsai-headstageportcontroldev"><span class="std std-ref">HeadstagePortControlDevice</span></a> node.</p>
</div>
<ul class="simple">
<li><p>Any workflows containing the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.html#bonsai-neuropixelsv1edev"><span class="std std-ref">NeuropixelsV1eDevice</span></a> node require the
<a class="reference internal" href="../Hardware%20Guide/Headstages/headstage-neuropix-1e.html#headstage-neuropix1e"><span class="std std-ref">Neuropixels-1.0e Headstage</span></a> to be connected before the workflows can be opened or
loaded into Bonsai.</p></li>
</ul>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>Check that the voltage set to the headstage port is correct for the
<a class="reference internal" href="../Hardware%20Guide/Headstages/headstage-neuropix-1e.html#headstage-neuropix1e"><span class="std std-ref">Neuropixels-1.0e Headstage</span></a> by using a workflow of a single <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/ONIContext.html#bonsai-onicontext"><span class="std std-ref">ONIContext</span></a>
node to configure it before connecting the headstage in order to open a workflow that
contains the <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.html#bonsai-neuropixelsv1edev"><span class="std std-ref">NeuropixelsV1eDevice</span></a> node.</p>
</div>
<ul class="simple">
<li><p>An <a class="reference internal" href="../Software%20Guide/Bonsai.ONIX/Nodes/ONIContext.html#bonsai-onicontext"><span class="std std-ref">ONIContext</span></a> node or any device node in a workflow can override device
settings in another workflow if device addresses are not distinct, because these nodes
read/write directly to hardware.</p></li>
</ul>
<section id="headstage-voltages">
<h2>Headstage Voltages<a class="headerlink" href="#headstage-voltages" title="Link to this heading">#</a></h2>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p><strong>Only have one workflow open at a time.</strong></p>
<p><strong>Ensure each headstage is configured with the correct voltage.</strong> Although
headstages are quite tolerate of over-voltage and under-voltage conditions,
they are only guaranteed to function within a specified range. When using
long and/or thin tethers, the voltage drop across the cable can become
significant. For more details, see <a class="reference internal" href="../Hardware%20Guide/Headstages/tether-voltage.html#tether-voltage"><span class="std std-ref">Headstage Voltages</span></a>.</p>
</div>
</section>
</section>
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</div>
<nav class="bd-toc-nav page-toc">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#hardware">Hardware</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#software">Software</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#breakout-board">Breakout Board</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#headstage-voltages">Headstage Voltages</a></li>
</ul>
</nav></div>

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