Update documentation

Author: actions-user

User-Manual/Plugins/LFP-Viewer.html

@@ -552,7 +552,7 @@ <h4>Thresholds<a class="headerlink" href="#thresholds" title="Permalink to this
 <h4>Channels<a class="headerlink" href="#channels" title="Permalink to this heading">#</a></h4>
 <ul class="simple">
 <li><p><strong>Reverse order:</strong> Displays the channels in opposite numerical order (highest-numbered channels at the top of the screen).</p></li>
-<li><p><strong>Sort by depth:</strong> Displays the channels by depth, if this information is available. Currently, there are no source nodes that include this information, although this will change soon.</p></li>
+<li><p><strong>Sort by depth:</strong> Displays the channels by depth, if this information is available. Currently, only the <a class="reference internal" href="Neuropixels-PXI.html#neuropixelspxi"><span class="std std-ref">Neuropixels PXI</span></a> plugin includes information about channel depth.</p></li>
 <li><p><strong>Skip:</strong> Sets the display to show every Nth channel. This is useful if you’re using a probe with many densely space contacts, and don’t need to visualize every one simultaneously.</p></li>
 <li><p><strong>Show number</strong>: Displays the channel indices, rather than the channel names, on the left-hand side of the LFP Viewer.</p></li>
 </ul>

User-Manual/Plugins/Probe-Viewer.html

@@ -537,6 +537,10 @@ <h3>Render modes<a class="headerlink" href="#render-modes" title="Permalink to t
 <li><p><strong>Spike Rate</strong> - Color corresponds to the number of threshold crossings per unit time within each pixel window. The threshold voltage can be adjusted.</p></li>
 </ol>
 </section>
+<section id="channel-ordering">
+<h3>Channel ordering<a class="headerlink" href="#channel-ordering" title="Permalink to this heading">#</a></h3>
+<p>The Probe Viewer will automatically sort channels by depth, if this information is available. Currently, the <a class="reference internal" href="Neuropixels-PXI.html#neuropixelspxi"><span class="std std-ref">Neuropixels PXI</span></a> plugin is the only upstream plugin that tags channels with depth information. Therefore, if you are using Neuropixels probes, the Probe Viewer will first sort channels by shank, and then by depth within each shank. Note that since channels not mapped to contiguous electrodes on Neuropixels 2.0 probes, this will result in the channels appearing “out of order” in the Probe Viewer display.</p>
+</section>
 </section>
 <section id="anatomy-overlay">
 <h2>Anatomy overlay<a class="headerlink" href="#anatomy-overlay" title="Permalink to this heading">#</a></h2>
@@ -647,6 +651,7 @@ <h3>Via config messages<a class="headerlink" href="#via-config-messages" title="
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#recommended-signal-chain">Recommended signal chain</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#plugin-configuration">Plugin configuration</a><ul class="nav section-nav flex-column">
 <li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#render-modes">Render modes</a></li>
+<li class="toc-h3 nav-item toc-entry"><a class="reference internal nav-link" href="#channel-ordering">Channel ordering</a></li>
 </ul>
 </li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#anatomy-overlay">Anatomy overlay</a><ul class="nav section-nav flex-column">

_sources/User-Manual/Plugins/LFP-Viewer.rst.txt

@@ -73,7 +73,7 @@ Channels
 
 * **Reverse order:** Displays the channels in opposite numerical order (highest-numbered channels at the top of the screen).
 
-* **Sort by depth:** Displays the channels by depth, if this information is available. Currently, there are no source nodes that include this information, although this will change soon.
+* **Sort by depth:** Displays the channels by depth, if this information is available. Currently, only the :ref:`neuropixelspxi` plugin includes information about channel depth.
 
 * **Skip:** Sets the display to show every Nth channel. This is useful if you're using a probe with many densely space contacts, and don't need to visualize every one simultaneously.
 

_sources/User-Manual/Plugins/Probe-Viewer.rst.txt

@@ -50,6 +50,10 @@ Render modes
 
 3. **Spike Rate** - Color corresponds to the number of threshold crossings per unit time within each pixel window. The threshold voltage can be adjusted.
 
+Channel ordering
+----------------
+
+The Probe Viewer will automatically sort channels by depth, if this information is available. Currently, the :ref:`neuropixelspxi` plugin is the only upstream plugin that tags channels with depth information. Therefore, if you are using Neuropixels probes, the Probe Viewer will first sort channels by shank, and then by depth within each shank. Note that since channels not mapped to contiguous electrodes on Neuropixels 2.0 probes, this will result in the channels appearing "out of order" in the Probe Viewer display.
 
 Anatomy overlay
 #####################