Spelling / Grammar Check and Link Check

bparks13 · bparks13 · commit f11c39dbe70b · 2024-02-13T14:26:25.000-05:00
Edited spelling and grammar, fixed broken links to external websites, and cleaned up broken/missing references for internal pages
diff --git a/README.rst b/README.rst
@@ -30,8 +30,8 @@ then you can build the documentation
 
    pipenv run make html
 
-if you want run ``make`` multiple times, prepend ``pipenv run`` on each command can be annoying,
-you can spawn a subshell with
+if you want to run ``make`` multiple times, prepending ``pipenv run`` on each command can be annoying.
+You can spawn a subshell with
 
 .. code:: shell
 
diff --git a/source/Hardware Guide/Adapters & EIBs/eib-64-large.rst b/source/Hardware Guide/Adapters & EIBs/eib-64-large.rst
@@ -22,6 +22,7 @@ The EIB pinout (ADC input mapping, stimulation connections, etc) is located on
 Tetrode Connectorization
 ****************************
 This EIB uses `Neuralynx "large" gold pins
-<https://neuralynx.com/hardware/large-eib-pins>`_ to attach tetrode wires.
+<https://neuralynx.fh-co.com/research-hardware/animal-interfaces/microdrive-preparation/large-eib-pins/>`_ 
+to attach tetrode wires.
 Usage instructions are provided in the `Neuralynx EIB pin Manual
 <https://neuralynx.com/documents/EIB%20Pins%20Manual.pdf>`_.
diff --git a/source/Hardware Guide/Adapters & EIBs/eib-64.rst b/source/Hardware Guide/Adapters & EIBs/eib-64.rst
@@ -32,6 +32,7 @@ The EIB pinout (ADC input mapping, stimulation connections, etc) is located on
 Tetrode Connectorization
 ****************************
 This EIB uses `Neuralynx "small" gold pins
-<https://neuralynx.com/hardware/small-eib-pins>`_ to attach tetrode wires.
+<https://neuralynx.fh-co.com/research-hardware/animal-interfaces/microdrive-preparation/small-eib-pins/>`_ 
+to attach tetrode wires.
 Usage instructions are provided in the `Neuralynx EIB pin Manual
 <https://neuralynx.com/documents/EIB%20Pins%20Manual.pdf>`_.
diff --git a/source/Hardware Guide/Adapters & EIBs/nano-z-adapter-64.rst b/source/Hardware Guide/Adapters & EIBs/nano-z-adapter-64.rst
@@ -4,7 +4,7 @@
 #########################
 **64-Channel Nano Z Adapter** is an adapter board that allows :ref:`eib_64`,
 :ref:`eib_64_large`, and :ref:`omnetics_adapter_64` to be used with the
-`Nano-Z <http://www.white-matter.com/products/nanoz/>`__ electrode impedance tester and
+`Nano-Z <https://white-matter.com/products/nanoz/>`__ electrode impedance tester and
 plating device. 
 
 .. figure:: /_static/images/nanoz-adapter-64_1r0.png
diff --git a/source/Hardware Guide/Breakout Board/index.rst b/source/Hardware Guide/Breakout Board/index.rst
@@ -48,5 +48,5 @@ Additionally, it has the following features:
   tables
 - 19" rack compatibility
 - Fully open-source gateware and made using an open-source FPGA toolchain
-  (`yosys <http://www.clifford.at/yosys/>`__ & `nextpnr
+  (`yosys <https://yosyshq.net/yosys/>`__ & `nextpnr
   <https://github.com/YosysHQ/nextpnr>`__)
diff --git a/source/Hardware Guide/Breakout Board/setup.rst b/source/Hardware Guide/Breakout Board/setup.rst
@@ -126,7 +126,7 @@ digital input serialization, digital output deserialization, interpreting user
 input, and driving indication LEDs. The `breakout board gateware
 <https://github.com/open-ephys/onix-breakout/tree/main/gateware>`__ is
 impelemented using an open-source toolchain (`Yosys
-<http://www.clifford.at/yosys/>`__ and `NextPnR
+<https://yosyshq.net/yosys/>`__ and `NextPnR
 <https://github.com/YosysHQ/nextpnr>`__).
 
 
diff --git a/source/Hardware Guide/Commutators/index.rst b/source/Hardware Guide/Commutators/index.rst
@@ -12,7 +12,7 @@ freely moving recordings with headstages and/or miniscopes.
     setup
     usage
 
-:Design Repository: https://github.com/open-ephys/onix-commutator
+:Design Repository: https://github.com/open-ephys/commutators
 :Compatibility: :ref:`pcie_host`, :ref:`headstage_64`,
                 :ref:`headstage_neuropix1`, :ref:`miniscopes`
 
diff --git a/source/Hardware Guide/Commutators/usage.rst b/source/Hardware Guide/Commutators/usage.rst
@@ -95,13 +95,13 @@ The controller firmware runs on a `Teensy
 3.2 <https://www.pjrc.com/store/teensy32.html>`__. To compile this firmware and
 program the microcontroller, you need the following dependencies:
 
-- `Arduino IDE <https://www.arduino.cc/en/Main/Software>`__
+- `Arduino IDE <https://www.arduino.cc/en/software/>`__
 - `Teensyduino add-on <https://www.pjrc.com/teensy/td_download.html>`__
 - `AccelStepper <https://www.airspayce.com/mikem/arduino/AccelStepper/>`__
 - `Arduino JSON <https://arduinojson.org/>`__
 
 The firmware can be uploaded to the device using the `Arduino
-IDE <https://www.arduino.cc/en/Main/Software>`__. 
+IDE <https://www.arduino.cc/en/software/>`__. 
 
 .. note:: You will need to add the `Teensyduino add-on
    <https://www.pjrc.com/teensy/teensyduino.html>`__ to the Arduino IDE to program
diff --git a/source/Hardware Guide/Datasheets/bno055.rst b/source/Hardware Guide/Datasheets/bno055.rst
@@ -14,7 +14,7 @@ The **BNO055** is a 9-axis inertial measurement unit (IMU) that provides
 orientation and acceleration information. At is core, this device corresponds
 to a single chip:
 
-- `BNO055 <https://www.bosch-sensortec.com/products/smart-sensors/bno055.html>`__
+- `BNO055 <https://www.bosch-sensortec.com/products/smart-sensors/bno055/>`__
   9-Axis IMU
 
 This device implementation has hard-coded all of the configuration required to
diff --git a/source/Hardware Guide/Datasheets/rhs2116.rst b/source/Hardware Guide/Datasheets/rhs2116.rst
@@ -143,7 +143,7 @@ Unmanaged Registers
 ------------------------------------------
 Read and write access is provided to the registers detailed in the `RHS2116
 series datasheet
-<https://intantech.com/files/Intan_RHS2116_series_datasheet.pdf>`__.
+<https://intantech.com/files/Intan_RHS2116_datasheet.pdf>`__.
 
 - Registers are 32-bits wide
 - Addresses and functions are determined by the RHS2116 datasheet
diff --git a/source/Hardware Guide/Datasheets/ts4231-v1-array.rst b/source/Hardware Guide/Datasheets/ts4231-v1-array.rst
@@ -15,10 +15,10 @@ that provides 3D position information. At is core, this device comprises an
 array of optical to digital converters that work with both V1 and V2 ("Index")
 and Steam/HTC/Vive base stations:
 
-- `TS4231 <https://triadsemi.com/product/ts4231/>`__ Optical to digital converter
+- **TS4231**: Optical to digital converter
 
 This device transmits data every time one of the sensors in the array receives
-and optical signal. The host computer must perform the mathematics in order to
+an optical signal. The host computer must perform the mathematics in order to
 calculate positional information using these data.
 
 .. _onidatasheet_ts4231_v1_array_reg:
diff --git a/source/Hardware Guide/Headstages/headstage-64/index.rst b/source/Hardware Guide/Headstages/headstage-64/index.rst
@@ -135,7 +135,7 @@ to set up tracking,
 3D Orientation Tracking
 *************************
 headstage-64 has a `BNO055
-<https://www.bosch-sensortec.com/products/smart-sensors/bno055.html>`_ 9-axis
+<https://www.bosch-sensortec.com/products/smart-sensors/bno055/>`_ 9-axis
 inertial measurement unit that provides the absolute orientation of the
 headstage. This device produces orientation (and other) measurements are 100
 Hz.
@@ -195,4 +195,4 @@ Bill of Materials
   sheet
   <https://docs.google.com/spreadsheets/d/1F-KWcdvH_63iXjZf0cgCfDiFX6XXW3qw6rlR8DZrFpQ/edit#gid=138167638>`__
 
-.. note:: Have a look at the :ref:`tether-voltage` page for more details on probing and verifying headstage power voltages 
+.. note:: Have a look at the :ref:`tether_voltage` page for more details on probing and verifying headstage power voltages 
diff --git a/source/Hardware Guide/Headstages/headstage-neuropix-1.rst b/source/Hardware Guide/Headstages/headstage-neuropix-1.rst
@@ -3,7 +3,7 @@
 Neuropixels-1.0 Headstage
 ##############################
 The ONIX **Neuropixels-1.0 Headstage** is a serialized, multifunction headstage
-targeting `Neuropixels 1.0 probes <https://www.neuropixels.org/probe>`__.
+targeting `Neuropixels 1.0 probes <https://www.neuropixels.org/>`__.
 
 .. image:: /_static/images/headstage-neuropix1/headstage-neuropix1_1r2_side-with-probes.jpg
     :align: center
diff --git a/source/Hardware Guide/Headstages/headstage-neuropix-1e.rst b/source/Hardware Guide/Headstages/headstage-neuropix-1e.rst
@@ -3,7 +3,7 @@
 Neuropixels-1.0e Headstage
 ##############################
 The ONIX **Neuropixels-1.0e Headstage** is a serialized, multifunction headstage
-targeting `Neuropixels 1.0 probes <https://www.neuropixels.org/probe>`__.
+targeting `Neuropixels 1.0 probes <https://www.neuropixels.org/>`__.
 
 .. image:: /_static/images/headstage-neuropix1e/headstage-np1e-with-probe.webp
     :align: center
diff --git a/source/Hardware Guide/Headstages/serialization.rst b/source/Hardware Guide/Headstages/serialization.rst
@@ -27,7 +27,7 @@ flexible. We generally use cables that are 150-300 μm in diameter.
 ONIX headstages use an FPGA to control peripheral devices and combine their
 data streams prior to serialization. For instance, :ref:`headstage_64` and
 :ref:`headstage_neuropix1` use an `Intel MAX10 FPGA
-<https://www.intel.com/content/www/us/en/products/programmable/fpga/max-10.html>`_.
+<https://www.intel.com/content/www/us/en/products/details/fpga/max/10.html>`_.
 The exact FPGA is not important because every ONI-compliant headstage is uses
 very similar gateware (FPGA-based firmware) that performs three major functions
 
diff --git a/source/Hardware Guide/Headstages/tethers.rst b/source/Hardware Guide/Headstages/tethers.rst
@@ -22,7 +22,7 @@ RF Loss in the 1 GHz regime.
 .. note:: Although the actual quantities matter, and **smaller values are
     better**, the major hurdle is simply finding a supplier that will clearly
     characterize them as this an indication of quality. We have used cables
-    from Axon Cable and `cooner wire <http://www.coonerwire.com/mini-coax/>`__
+    from Axon Cable and `cooner wire <https://www.coonerwire.com/mini-coax/>`__
     with good results.
 
 :DC Resistance: For DC signals, resistance is proportional to the inner
diff --git a/source/Hardware Guide/PCIe Host/bracket-assembly.rst b/source/Hardware Guide/PCIe Host/bracket-assembly.rst
@@ -1,5 +1,8 @@
 .. _pcie_host_bracket_assembly:
 
+.. toctree::
+    :hidden:
+    
 PCIe Bracket Assembly
 ########################################
 
@@ -18,7 +21,7 @@ Materials
       - Notes
     * - 3D printed bracket
       - 1
-      - `STL file <https://github.com/open-ephys/onix-fmc-host/blob/main/mechanical/pcie-bracket/stl/pcie-bracket-1p27mm.STL>`__
+      - `STL file <https://github.com/open-ephys/onix-fmc-host/blob/main/mechanical/pcie-bracket-3dprint/stl/pcie-bracket-1p27mm.STL>`__
       - Sintered Nylon. Glass-bead reinforced is even better
     * - 3mm light pipe
       - 2
diff --git a/source/Hardware Guide/PCIe Host/multi-board-sync.rst b/source/Hardware Guide/PCIe Host/multi-board-sync.rst
@@ -1,5 +1,8 @@
 .. _pcie_host_multiboard_sync:
 
+.. toctree::
+    :hidden:
+    
 Synchronizing Multiple PCIe Hosts
 ########################################
 
diff --git a/source/Hardware Guide/PCIe Host/overview.rst b/source/Hardware Guide/PCIe Host/overview.rst
@@ -1,5 +1,8 @@
 .. _pcie_host_overview:
 
+.. toctree::
+    :hidden:
+    
 Overview
 #########################
 The **ONIX PCIe Host** combines the `ONIX FMC Host Module
diff --git a/source/Hardware Guide/PCIe Host/setup-windows.rst b/source/Hardware Guide/PCIe Host/setup-windows.rst
@@ -1,5 +1,8 @@
 .. _pcie_host_setup_windows:
 
+.. toctree::
+    :hidden:
+    
 Setup Guide for Windows
 ########################################
 
diff --git a/source/Hardware Guide/PCIe Host/updating-firmware.rst b/source/Hardware Guide/PCIe Host/updating-firmware.rst
@@ -1,10 +1,13 @@
 .. _pcie_host_firmware_update:
 
+.. toctree::
+    :hidden:
+    
 Updating Firmware in Windows
 ########################################
 
 #. If you have not done so already, follow the steps on the
-   :ref:`pcie_host_setup_windows` page.
+   :ref:`Setup Guide for Windows <pcie_host_setup_windows>` page.
 
 #. Download the latest :ref:`oni_repl_download` and unzip it. Navigate to this
    location using a console (e.g. PowerShell).
diff --git a/source/Hardware Guide/index.rst b/source/Hardware Guide/index.rst
@@ -25,7 +25,7 @@ ONIX consists of several hardware devices:
     Datasheets/index
     Connections & Cables/index
 
-:ref:`pcie_host`
+:ref:`PCIe Host<pcie_host>`
 -----------------------------------------
 The ONIX PCIe/FMC host device is the heart of ONIX. It provides the interface
 between the acquisition computer and any attached headstages, as well as
@@ -37,7 +37,7 @@ reducing closed-loop latencies.
 The host can also generate a very precise clock that is synchronized to its
 hardware.
 
-:ref:`breakout`
+:ref:`Breakout<breakout>`
 -----------------------------------------
 The Breakout Board facilitates user access to the functionality of the host
 board. On the Breakout Board, the analog channels and digital lines of the host
@@ -49,31 +49,31 @@ Headstages can be connected directly to the host, or with an SMA connection
 first to the Breakout Board and then to the host. The same can be done to
 access the host clock output.
 
-:ref:`headstages` & :ref:`miniscopes`
------------------------------------------
+:ref:`Headstages<headstages>` & :ref:`Miniscopes<miniscopes>`
+--------------------------------------------------------------------
 ONIX headstages communicate with the host board through a coaxial cable, that
 can be kept very thin and light. Rather than just pre-amplifying data, ONIX
 headstages perform many tasks on the headstage itself. The 64-channel
 headstage, for instance, can locally drive an LED or provide current
 stimulation, without the need for an external device and an additional fiber or
 cable to the animal. UCLA Miniscopes are also directly compatible with ONIX.
 
-:ref:`commutators`
+:ref:`Commutators<commutators>`
 -----------------------------------------
 The active commutator is optional, but very useful for experiments with
 freely-moving animals. The commutator responds to the orientation sensor in the
 headstage or miniscope. When the animal turns, the commutator can actively turn
 a rotary joint, precisely counteracting the rotation of the animal and
 preventing twisting of the tether.
 
-:ref:`lighthouses`
+:ref:`Lighthouses<lighthouses>`
 -----------------------------------------
 Lighthouses or 'base stations' are positioned above the setup. They emit either
 a vertical or horizontal laser plane that sweeps over the setup. Trackable ONIX
 headstages contain infrared diodes that detect this light, allowing the spatial
 position of the photodiode to be determined.
 
-:ref:`adapters_eibs`
+:ref:`Adapters & EIBs<adapters_eibs>`
 -----------------------------------------
 Several adapters and EIBs exist to interface between ONIX and
 microwire or silicon probes, as well as an adapter for Omnetics-based
diff --git a/source/Software Guide/Bonsai.ONIX/GettingStarted.rst b/source/Software Guide/Bonsai.ONIX/GettingStarted.rst
@@ -33,7 +33,7 @@ Bonsai Learning Resources
       - Bonsai's Q/A forum with **lots** of useful examples and solutions for
         various common (and uncommon) acquisition scenarios.
 
-    * - `ReactiveX operator definitions  <http://reactivex.io/documentation/operators.html>`__
+    * - `ReactiveX operator definitions  <https://reactivex.io/documentation/operators.html>`__
       - Detailed information on many of the reactive operators you will find in
         Bonsai's Reactive library, especially in the "Combinators" grouping
 
diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/AnalogIODevice.rst b/source/Software Guide/Bonsai.ONIX/Nodes/AnalogIODevice.rst
@@ -5,20 +5,15 @@ AnalogIODevice
 A `Bonsai source <https://bonsai-rx.org/docs/editor/#toolbox>`__ that wraps a
 :ref:`onidatasheet_fmc_analog_io` device.
 
-:Inputs:  A 12xN `OpenCV.Net.Mat
-          <https://www.fuget.org/packages/OpenCV.Net/3.4.0-build001/lib/netstandard2.0/OpenCV.Net.dll/OpenCV.Net/Mat>`__
+:Inputs:  A 12xN **OpenCV.Net.Mat**
 
           - Each column contains 12 analog values, one for each channel.
           - If a channel is set to an input, this will have no effect.
           - Data is immediately consumed by hardware. If N > 1, then samples
             will be produced as quickly as hardware allows.
-          - The matrix must contain elements with `Depth.S16
-            <https://www.fuget.org/packages/OpenCV.Net/3.4.0-build001/lib/netstandard2.0/OpenCV.Net.dll/OpenCV.Net/Depth>`__
-            when
-            the ``DataType`` parameter is set to is "S16" and either `Depth.F32
-            or Depth.F64
-            <https://www.fuget.org/packages/OpenCV.Net/3.4.0-build001/lib/netstandard2.0/OpenCV.Net.dll/OpenCV.Net/Depth>`__
-            when ``DataType`` is set to "Volts".
+          - The matrix must contain elements with **Depth.S16**
+            when the ``DataType`` parameter is set to is "S16" and either **Depth.F32**
+            or **Depth.F64** when ``DataType`` is set to "Volts".
           - When the ``DataType`` parameter is set to is "S16", analog output voltages
             are encoded in offset binary, with 0 resulting in -10V and 65355
             resulting in +10V.
@@ -30,8 +25,7 @@ A `Bonsai source <https://bonsai-rx.org/docs/editor/#toolbox>`__ that wraps a
             <onidatasheet_heartbeat_d2h>`.
           - The number of samples in each output is determined by the
             ``BlockSize`` parameter
-          - Analog voltages are packaged into 12xBlockSize `OpenCV.Net.Mat
-            <https://www.fuget.org/packages/OpenCV.Net/3.4.0-build001/lib/netstandard2.0/OpenCV.Net.dll/OpenCV.Net/Mat>`__
+          - Analog voltages are packaged into 12xBlockSize (**OpenCV.Net.Mat**)
 
 .. raw:: html
 
diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst b/source/Software Guide/Bonsai.ONIX/Nodes/NeuropixelsV1eDevice.rst
@@ -60,7 +60,7 @@ Parameters available through the property pane are as follows:
 
     * - RequireSNMatch
       - boolean
-        If True, the configuration and probe serial numbers must match
+      - If True, the configuration and probe serial numbers must match
         to start acquisition. Keeping this parameter set to True is good
         practice because the correct calibration files must be loaded in order
         for the probe to function properly.
diff --git a/source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst b/source/Software Guide/Bonsai.ONIX/Nodes/ONIContext.rst
@@ -14,7 +14,7 @@ There must be at least one of these in every workflow that uses ONIX hardware.
 
 :Inputs:  None
 :Outputs: A single ``ONIContextTask`` followed by `Never
-          <http://reactivex.io/documentation/operators/empty-never-throw.html>`__.
+          <https://reactivex.io/documentation/operators/empty-never-throw.html>`__.
 
 .. raw:: html
 
diff --git a/source/Software Guide/index.rst b/source/Software Guide/index.rst
@@ -3,16 +3,16 @@
 
 .. _software:
 
-|software_logo| Software Guide
-===================================
-
 .. toctree::
     :hidden:
 
     oni-repl/index
     Bonsai.ONIX/index
     Open Ephys GUI/index
 
+|software_logo| Software Guide
+===================================
+
 Although ONIX is software agnostic, we have focused our development efforts on `Bonsai <https://bonsai-rx.org/>`__ for data acquisition. Bonsai is
 very good at dealing with the asynchronous and heterogeneous data that ONIX
 hardware produces.
