Commutator tutorial

Pipfile

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 sphinx = "*"
 pydata-sphinx-theme = "0.13.3"
 sphinx-tabs = "*"
-make = "*"
+make = "*"
+sphinx-design = "*"

source/Tutorials/Commutator.rst

@@ -0,0 +1,117 @@
+.. _commutator:
+
+..  role:: raw-html-m2r(raw)
+    :format: html
+
+Automated Tether Commutation
+============================
+
+..  note::
+    Following this tutorial requires a 3D capable headstage, an Open Ephys SPI commutator, and a 3D capable data acquisition system (e.g. a Gen 3 Acquisition Board or an ONIX board).
+
+Most acquisition systems rely on a tether to transmit power and data between the headstage and the
+data acquisition system. This can be problematic during freely behaving experiments because the
+animal is liable to twist and tangle the tether while it moves around which can end up exerting
+torque on the animal. This is mitigated by using a commutator, a device that untwists the tether as
+the animal moves around while maintaining electrical continuity between the animal and data
+acquisition system. This encourage more naturalistic behaviors.
+
+This tutorial demonstrates how to automate commutation using a the Open Ephys GUI, a 3D-capable
+headstage, and an Open Ephys SPI commutator. 
+
+Hardware connections
+#####################
+
+..  tab-set::
+    :sync-group: acquisition-hardware
+
+    ..  tab-item:: Acquisition Board
+        :sync: acquisition-board
+
+        #.  Follow the `Acquisition Board Quick Start Guide
+            <https://open-ephys.github.io/acq-board-docs/User-Manual/Quickstart-guide.html>`__ to establish
+            the following acquisition board connections:
+
+            -   USB 3.0 connection between the acquisition board and the PC.
+
+            -   +5V connection between the acquisition board and an AC power source.
+
+        #.  Follow the `SPI Commutator Connections section
+            <https://open-ephys.github.io/commutator-docs/user-guide/mount-connect.html?commutator=spi#connecting>`__
+            of the commutator hardware docs to establish the following commutator connections:
+
+            -   SPI connection between the commutator's stator and the acquisition board.
+
+            -   SPI connection between the commutator's rotor and the 3D capable headstage.
+
+            -   USB connection between the commutator and the PC.   
+
+    ..  tab-item:: ONIX
+        :sync: onix
+
+        #.  Follow the `ONIX Hardware Guide
+            <https://open-ephys.github.io/onix-docs/User-Manual/Quickstart-guide.html>`__ to setup
+            your ONIX board and establish the following ONIX system's connections:
+
+            -   2x (A & B) coaxial connections between the breakout board and the PCIe host.
+
+            -   SDR connection between the breakout board and the PCIe host.
+
+        #.  Follow the `Coax Commutator Connections section
+            <https://open-ephys.github.io/commutator-docs/user-guide/mount-connect.html?commutator=coax#connecting>`__
+            of the commutator hardware docs to establish the connections between the ONIX system and a 3D capable headstage:
+
+            -   Coaxial connection between the commutator's stator and the acquisition board.
+
+            -   Coaxial connection between the commutator's rotor and the 3D capable headstage.
+
+            -   USB connection between the commutator and the PC.   
+
+
+Install GUI and prepare signal chain
+####################################
+
+#.  :doc:`Install the Open Ephys GUI </User-Manual/Installing-the-GUI>` if you haven't already.
+
+#.  Open the GUI. 
+
+    ..  note::
+        -   If this is your first time opening the GUI, you will be queried to load a default signal chain. Choose the "Acquisition Board" signal chain.
+        -   If the Open Ephys GUI already has a signal chain loaded you would like to save, :ref:`do that <file>` before proceeding to the next step because the next step overwrites any current signal chain.
+
+#.  Download one following signal chains depending on which hardware you are using.
+
+    ..  tab-set::
+        :sync-group: acquisition-hardware
+
+        ..  tab-item:: Acquisition Board
+            :sync: acquisition-board
+
+            :download:`Acquisition Board Signal Chain`
+
+            ..  image:: /_static/images/tutorials/commutator/onix-signal-chain.png
+                :alt: Acquisition Board Signal Chain for commutation
+
+        ..  tab-item:: ONIX
+            :sync: onix
+
+            :download:`ONIX Signal Chain`
+
+            ..  image:: /_static/images/tutorials/commutator/onix-signal-chain.png
+                :alt: ONIX Signal Chain for commutation
+
+#.  :ref:`Open <file>` the downloaded signal chain in the GUI.
+
+#.  Refer to :doc:`/User-Manual/Plugins/Commutator-Control` to configure the Commutator Control
+    processor.
+
+    -   The selected stream should correspond to a port that has a 3D capable headstage to it.
+
+    -   The selected COM port should correspond to the one to which your commutator is connected. 
+
+    -   For an off-the-shelf Open Ephys 3D capable headstage, adjusting the rotation axis is not
+        necessary.
+
+#.  Click the ▶ play button in the top-right corner of the GUI. The commutator now follows the
+    rotation of the headstage. 
+

source/Tutorials/index.rst

@@ -18,6 +18,7 @@ The following tutorials are available for the Open Ephys GUI:
 
     Closed-Loop-Latency
     Data-Synchronization
+    Commutator
     How-To-Make-Your-Own-Plugin
     Making-Your-Own-Visualizer-Plugin
 

source/User-Manual/Exploring-the-user-interface.rst

@@ -87,6 +87,8 @@ Menu items
 
 Below you'll find documentation for all of the commands available from the GUI's menu:
 
+.. _file:
+
 File
 -----
 * **Open**: Browse for a previously saved signal chain XML file, and load it into the GUI.

source/User-Manual/Plugins/Commutator-Control.rst

@@ -9,7 +9,7 @@ Commutator Control
 ..  image:: ../../_static/images/plugins/commutatorcontrol/oecommutator.png
     :alt: Annotated settings interface for the Commutator Control plugin
 
-..  csv-table:: Prevents twist in the tether connecting a moving animal to a stationary `Open Ephys acquisition board Gen3 <https://open-ephys.org/acq-board>`__.
+..  csv-table:: Prevents twist in the tether connecting a moving animal to a stationary `Open Ephys acquisition board Gen3 <https://open-ephys.org/acq-board>`__ using orientation data collected from a 3D-capable headstage.
     :widths: 18, 80
 
     "*Plugin Type*", "Sink" 

source/conf.py

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 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = ["sphinx.ext.todo", 
-              "sphinx.ext.githubpages"]
+              "sphinx.ext.githubpages",
+              "sphinx_design"]
 
 
 # Add any paths that contain templates here, relative to this directory.