Headstage-64 Content and Various Minor Edits (#86)

* Update Admonitions
- No more red admonitions
- Only four admonitions: NOTE, TIP, IMPORTANT, WARNING

* Fix PortStatus Note

* Headstage Content and Various Minor Changes
- Requires ts4231, estim, & ostim pages and loading python script

api/configure.md

@@ -3,4 +3,4 @@ uid: configure
 title: Configuration Operators
 ---
 
-Configuration operators belong in a top-level chain of operators between [core operators](xref:core) ([`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition)) to configure ONIX hardware.
+Device configuration operators belong in a top-level chain of operators between [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to configure devices contained by ONIX hardware hubs.

api/device-configure.md

@@ -3,9 +3,9 @@ uid: device-configure
 title: Device Configuration Operators
 ---
 
-> [!CAUTION]
->  Device configuration operators are not recommended for using off-the-shelf Open Ephys hardware. Use [aggregate configuration operators](xref:configure) instead. [Aggregate configuration operators](xref:configure) confer the following benefits:
+> [!IMPORTANT]
+>  Device configuration operators are not recommended for using off-the-shelf Open Ephys hardware. Use aggregate [configuration operators](xref:configure) instead. Aggregate [configuration operators](xref:configure) confer the following benefits:
 > - The `address` and `name` properties of aggregate configuration operators undergo automatic configuration which reduces the risk of erroneous configuration.
 > - The workflow is less cluttered with configuration operators as one aggregate configuration operator corresponds to multiple device operators. This improves workflow legibility and expedites the workflow scripting process.
 
-Device configuration operators belong in a top-level chain of operators between [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to configure devices contained by ONIX hardware.
+Device configuration operators belong in a top-level chain of operators between [`CreateContext`](xref:OpenEphys.Onix1.CreateContext) and [`StartAcquisition`](xref:OpenEphys.Onix1.StartAcquisition) to configure devices contained by ONIX hardware hubs.

articles/hardware/breakout/configuration.md

@@ -11,7 +11,7 @@ videoCaption:
 workflowLocation: workflow
 ---
 
-## Configuring the breakout board
+## Configuring the Breakout Board
 The `ConfigureBreakoutBoard` operator groups the properties
 for all the devices that the breakout board supports. Each device in the
 property pane can be expanded to expose individual properties that govern their
@@ -44,4 +44,6 @@ breakout board example workflow:
 
 - The `BreakoutBoard`'s `AnalogIO Direction0` property is set to `Output`.
 - The `BreakoutBoard`'s `MemoryMonitor Enable` property is set to `True`.
-- The `BreakoutBoard`'s `OutputClock Gate` property is set to `True`.
+- The `BreakoutBoard`'s `OutputClock Gate` property is set to `True`.
+
+[!INCLUDE [timestamp-info](../../../includes/configuration-timestamp.md)]

articles/hardware/breakout/memory-monitor.md

@@ -1,7 +1,6 @@
 ---
 uid: breakout_memory-monitor
 title: Breakout Board Memory Monitor
-hardware: true
 device: memory monitor
 ---
 

articles/hardware/hs64/bno055.md

@@ -0,0 +1,8 @@
+---
+uid: hs64_bno055
+title: Headstage 64 Bno055
+hardware: Headstage 64
+bno055: true
+bnoOperator: Bno055Data
+hardwareOperator: Headstage 64
+---

articles/hardware/hs64/configuration.md

@@ -0,0 +1,19 @@
+---
+uid: hs64_configuration
+title: Headstage64 Configuration
+hardware: Headstage64
+configuration: true
+operator: ConfigureHeadstage64
+dataRate: 4.1
+timeUntilFullBuffer: 500 μs
+blockReadSize: 2048
+workflowLocation: workflow
+---
+
+## Configuring the Breakout Board and Headstage64
+
+The `ConfigureBreakoutBoard` operator configures the Onix Breakout Board. In the Headstage64 example tutorial, it is configured to enable digital inputs to serve as a trigger for the Headstage64's electrical and optical stimulation and to enable monitoring of the percentage of memory occupied. This is accomplished by leaving all of the `ConfigureBreakoutBoard` properties set to their default values except its `Memory Monitor` `Enable` property is set to `True`. 
+
+The `ConfigureHeadstage64` operator is used to configure the Headstage64. In the Headstage64 example tutorial, it is configured to enable streaming of electrophysiology data from a Rhd2164 amplifier, orientation data from the on-board Bno055 IMU, and position data from the Ts4231. This is accomplished in the Headstage64 example workflow by leaving all of the `ConfigureHeadstage64` properties set to their default values.
+
+[!INCLUDE [timestamp-info](../../../includes/configuration-timestamp.md)]

articles/hardware/hs64/estim.md

@@ -0,0 +1,10 @@
+---
+uid: hs64_estim
+title: Headstage 64 Electrical Stimulation
+---
+
+The following excerpt from the Headstage64 [example workflow](xref:hs64_hs64) demonstrates electrical stimulation.
+
+::: workflow
+![/workflows/hardware/hs64/estim.bonsai workflow](../../../workflows/hardware/hs64/estim.bonsai)
+:::

articles/hardware/hs64/memory-monitor.md

@@ -0,0 +1,29 @@
+---
+uid: hs64_memory-monitor
+title: Headstage64 Memory Monitor
+---
+
+The following excerpt from the Breakout Board [example workflow](xref:breakout_workflow) demonstrates memory monitor functionality and saves memory monitor data.
+
+::: workflow
+![/workflows/hardware/breakout/memory-monitor.bonsai workflow](../../../workflows/hardware/breakout/memory-monitor.bonsai)
+:::
+
+The <xref:OpenEphys.Onix1.MemoryMonitorData> operator generates a sequence of <xref:OpenEphys.Onix1.MemoryMonitorDataFrame>s. `MemoryMonitorData` emits `MemoryMonitorDataFrame`s at a regular interval defined during <xref:breakout_configuration> using the <xref:OpenEphys.Onix1.ConfigureBreakoutBoard>'s `MemoryMonitor SamplesPerSecond` property (in our case 10 Hz). In the Breakout Board example workflow, the `MemoryMonitorData`'s `DeviceName` property is set to "BreakoutBoard/MemoryMonitor". This links the `MemoryMonitorData` operator to the corresponding configuration operator. The [CsvWriter](https://bonsai-rx.org/docs/api/Bonsai.IO.CsvWriter.html) operator saves the `Clock`, `BytesUsed`, and `PercentUsed` members to a file with the following format: `memory-use_<timestamp>.csv`. Because `CsvWriter` is a _sink_ operator, its output sequence is equivalent to its input sequence. In other words, its output is equivalent to `MemoryMonitorData`'s output. Therefore, it's possible to use a [MemberSelector](https://bonsai-rx.org/docs/api/Bonsai.Expressions.MemberSelectorBuilder.html) operator on the `CsvWriter` to select members from the `MemoryMonitorDataFrame`. The `MemberSelector` operator selects the `PercentUsed` member from the `MemoryMonitorDataFrame` so the user can visualize `PercentUsed` data from the `MemoryMonitorDataFrame`.
+
+> [!NOTE]
+> The `MemoryMonitorDataFrame` operator generates a
+> data stream that is most useful in the context of closed-loop performance. It tells the user if data
+> is being consumed rapidly enough by the host PC to keep up with data production by the hardware. The
+> hardware FIFO is a buffer that is required to deal with the fact that computers with normal
+> operating systems cannot perform operations with strict regularity. When there are hiccups in
+> acquisition, the hardware FIFO picks up the slack, but should then be cleared immediately. To get
+> the lowest latencies, the `BlockReadSize` should be as small as possible *while the memory use
+> percentage remains around 0%*.
+
+> [!WARNING]
+> If the hardware FIFO's `PercentUsed` is non-zero for long time periods, or is increasing, the
+> `StartAcquisition`'s `BlockReadSize` setting is too small (see the [breakout board configuration](xref:breakout_configuration)). A small
+> `BlockReadSize` will mean that the host computer does not have to wait long for enough data to
+> become available to propagate it forward, but will reduce overall bandwidth by increasing the
+> frequency at which the host computer checks if data is available and performs hardware reads.

articles/hardware/hs64/ostim.md

@@ -0,0 +1,11 @@
+---
+uid: hs64_ostim
+title: Headstage 64 Optical Stimulation
+---
+
+The following excerpt from the Headstage64 [example workflow](xref:hs64_hs64) demonstrates optical stimulation.
+
+::: workflow
+![/workflows/hardware/hs64/ostim.bonsai workflow](../../../workflows/hardware/hs64/ostim.bonsai)
+:::
+

articles/hardware/hs64/overview.md

@@ -0,0 +1,29 @@
+---
+uid: hs64_hs64
+title: Headstage 64
+---
+
+These are the devices available on the Headstage64:
+
+- [Rhd2164](xref:hs64_rhd2164):
+    - 64 electrophysiology channels for passive probes (e.g. tetrode, silicon probe, etc.) sampled at 30 kHz with 16 bit depth
+    - Adjustable analog band-pass filter:
+      - Lower cutoff configurable from 0.1 Hz to 500 Hz
+      - Upper cutoff configurable from 100 Hz to 20 kHz
+    - Optional adjustable digital high-pass filter with cutoff configurable from 0.146 Hz to 3309 Hz
+    - Three auxiliary ADC channels sampled at 30 kHz with 16 bit depth
+- [Bno055](xref:hs64_bno055): 9-axis IMU for real-time, 3D orientation tracking sampled up to ~100 Hz for easy automated commutation with Open Ephys commutators
+- [Ts4231](xref:hs64_ts4231): For compatibility with HTC Vive Lighthouses for real-time, 3D position tracking
+- [Electrical Stimulation](xref:hs64_estim): Single current source with ±15V compliance voltage and automatic electrode discharge
+    - The stimulation waveform is highly configurable via the <xref:OpenEphys.Onix1.Headstage64ElectricalStimulatorTrigger>'s properties.
+- [Optical Stimulation](xref:hs64_ostim): Two current sources with 800mA upper limit
+    - The stimulation waveform is highly configurable via the <xref:OpenEphys.Onix1.Headstage64OpticalStimulatorTrigger>'s properties.
+
+> [!TIP]
+> For a detailed explanation of the Rhd2164 amplifier's properties, read the [datasheet](https://intantech.com/files/Intan_RHD2164_datasheet.pdf). 
+
+> [!TIP]
+> Visit the [Headstage64 Hardware Guide](https://open-ephys.github.io/onix-docs/Hardware%20Guide/Headstages/headstage-64/index.html) to learn more about the hardware such as weight, dimensions, and proper power voltages.
+
+The following pages in the Headstage64 Guide provide an example workflow and a
+breakdown of its components.

articles/hardware/hs64/port-status.md

@@ -0,0 +1,9 @@
+---
+uid: hs64_port-status
+title: Headstage 64 Port Status
+hardware: Headstage 64
+portStatus: true
+configureHardwareOperator: ConfigureHeadstage64
+hardwareOperator: Headstage64
+---
+

articles/hardware/hs64/rhd2164.md

@@ -0,0 +1,16 @@
+---
+uid: hs64_rhd2164
+title: Headstage64 Rhd2164
+---
+
+The following excerpt from the Headstage64 [example workflow](xref:hs64_hs64) demonstrates the Rhd2164 functionality by streaming and saving data from the Rhd2164 device.
+
+::: workflow
+![/workflows/hardware/hs64/rhd2164.bonsai workflow](../../../workflows/hardware/hs64/rhd2164.bonsai)
+:::
+
+The <xref:OpenEphys.Onix1.Rhd2164Data> operator generates a sequence of <xref:OpenEphys.Onix1.Rhd2164DataFrame>s using the following settings:
+- `BufferSize` is set to 30. Each `Rhd2164DataFrame` will contain a [1 x 30 sample] `Clock` vector, a [64 channel x 30 sample] `AmplifierData` matrix, and a [3 channel x 30 sample] `AuxData` matrix. This corresponds to 1.2 ms of data per data frame.
+- The `Headstage64Data`'s `DeviceName` property is set to "Headstage64/Rhd2164". This links the `Rhd2164Data` operator to the corresponding configuration operator.
+
+The relevant properties are extracted from the `Rhd2164DataFrame` by right-clicking the `Rhd2164Data` operator, and choosing the following **Output** members: `Clock`, `AmplifierData`, and `AuxData`. The [`MatrixWriter`](https://bonsai-rx.org/docs/api/Bonsai.Dsp.MatrixWriter.html) operators saves the selected members to files with the following format: `rhd2164-clock_<timestamp>.raw`, `rhd2164-amplifier_<timestamp>.raw`, and `rhd2164-aux_<timestamp>.raw`, respectively.

articles/hardware/hs64/ts4231.md

@@ -0,0 +1,12 @@
+---
+uid: hs64_ts4231
+title: Headstage64 Position Data
+---
+
+The following excerpt from the Headstage64 [example workflow](xref:hs64_hs64) demonstrates electrical stimulation.
+
+::: workflow
+![/workflows/hardware/hs64/ts4231.bonsai workflow](../../../workflows/hardware/hs64/ts4231.bonsai)
+:::
+
+The <xref:OpenEphys.Onix1.TS4231V1PositionData> operator generates a sequence of <xref:OpenEphys.Onix1.TS4231V1PositionDataFrame>s.

articles/hardware/hs64/workflow.md

@@ -0,0 +1,17 @@
+---
+uid: hs64_workflow
+title: Headstage64 Example Workflow
+---
+
+The example workflow below can by copy/pasted into the Bonsai editor using the clipboard icon in the top right. This workflow:
+- Captures electrophysiology data from passive probes via the RHD2164 amplifier and saves it to disk.
+- Captures orientation data from the Bno055 IMU and saves it to disk.
+- Monitors the Headstage64 port status.
+- Automatically commutates the tether if there is a proper commutator connection. 
+- Applies electrical stimulation triggered by pressing the breakout board's ☾ key.
+- Applies optical stimulation triggered by pressing the breakout board's △ key.
+- Monitors memory usage data.
+
+::: workflow
+![/workflows/hardware/hs64/hs64.bonsai workflow](../../../workflows/hardware/hs64/hs64.bonsai)
+:::

articles/hardware/np1e/bno055.md

@@ -2,7 +2,7 @@
 uid: np1e_bno055
 title: NeuropixelsV1e Bno055
 hardware: NeuropixelsV1e Headstage
-device: true
 bno055: true
+bnoOperator: PolledBno055Data
 hardwareOperator: NeuropixelsV1eHeadstage
 ---

articles/hardware/np1e/configuration.md

@@ -1,6 +1,6 @@
 ---
 uid: np1e_configuration
-title: Neuropixels 1.0 Headstage Configuration
+title: NeuropixelsV1e Headstage Configuration
 hardware: NeuropixelsV1e Headstage
 configuration: true
 operator: ConfigureNeuropixelsV1eHeadstage
@@ -10,7 +10,7 @@ blockReadSize: 4096
 workflowLocation: overview
 ---
 
-## Configuring the NeuropixelsV1e headstage
+## Configuring the NeuropixelsV1e Headstage
 The `NeuropixelsV1eHeadstage` operator is used to configure the Neuropixels V1e Headstage; this can enable streaming of electrophysiology data from a Neuropixels 1.0 probe and orientation data from a Bno055 IMU. This is accomplished in the example workflow by leaving all of the `NeuropixelsV1eHeadstage` properties set to their default values.
 
 Default values for the headstage are:
@@ -21,8 +21,10 @@ Default values for the headstage are:
 - Enabling the `Spike Filter`
 - Setting the `Reference` to *External*
 
-> [!WARNING]
+> [!IMPORTANT]
 > The workflow will not run unless gain calibration and ADC calibration files are provided. Click the `NeuropixelsV1eHeadstage` operator, expand `NeuropixelsV1e` in the properties pane, then choose the appropriate files by selecting either `GainCalibrationFile` or `AdcCalibrationFile` and clicking the <kbd>...</kbd> button.
 
 > [!TIP]
 > For additional details on how to manually configure the headstage, such as enabling specific electrodes for recording, or modify AP / LFP gain, check out the <xref:np1e_gui> page.
+
+[!INCLUDE [timestamp-info](../../../includes/configuration-timestamp.md)]

articles/hardware/np1e/npv1e.md

@@ -2,7 +2,6 @@
 uid: np1e_npv1e
 title: NeuropixelsV1e
 hardware: NeuropixelsV1e Headstage
-device: true
 ---
 
 The following excerpt from the NeuropixelsV1e Headstage [example workflow](xref:np1e_npv1e-headstage) demonstrates NeuropixelsV1e functionality by streaming and saving probe data.

articles/hardware/np1e/overview.md

@@ -11,21 +11,19 @@ These are the devices available on the NeuropixelsV1e Headstage:
     - 384 parallel, dual-band (AP, LFP), low-noise recording channels.
         - AP band at 0.3-10 kHz, sampled at 30 kHz
         - LFP band at 0.5-500 Hz, sampled at 2.5 kHz
-- [Bno055](xref:np1e_bno055): 9-axis IMU for real-time, 3D orientation tracking, and easy automated commutation with Open Ephys commutators.
+- [Bno055](xref:np1e_bno055): 9-axis IMU for real-time, 3D orientation tracking sampled up to ~100 Hz for easy automated commutation with Open Ephys commutators.
 
 > [!TIP]
 > Visit the [NeuropixelsV1e Headstage Hardware Guide](https://open-ephys.github.io/onix-docs/Hardware%20Guide/Headstages/headstage-neuropix-1e.html) to learn more about the hardware such as weight, dimensions, and proper power voltages.
 
 The example workflow below can by copy/pasted into the Bonsai editor using the clipboard icon in the top right. This workflow:
-- Captures data from the Bno055 IMU and NeuropixelsV1e probe, saving all data to disk.
-- Monitors the the NeuropixelsV1e Headstage port status.
+- Captures electrophysiology data from the Neuropixels 1.0 probe and saves it to disk.
+- Captures orientation data from the Bno055 IMU and saves it to disk.
+- Monitors the NeuropixelsV1e Headstage port status.
 - Automatically commutates the tether if there is a proper commutator connection. 
 
 ::: workflow
 ![/workflows/hardware/np1e/np1e.bonsai workflow](../../../workflows/hardware/np1e/np1e.bonsai)
 :::
 
 The following pages in the Neuropixels V1e Headstage Guide provide a breakdown of the above example workflow.
-
-> [!TIP]
-> Visit the <xref:getting-started> pages if you are unfamiliar with Bonsai.

articles/hardware/np1e/port-status.md

@@ -1,8 +1,8 @@
 ---
 uid: np1e_port-status
-title: Port Status
+title: NeuropixelsV1e Headstage Port Status
 hardware: NeuropixelsV1e Headstage
-device: true
 portStatus: true
+configureHardwareOperator: ConfigureNeuropixelsV1eHeadstage
 hardwareOperator: NeuropixelsV1eHeadstage
 ---

articles/hardware/np2e/bno055.md

@@ -2,7 +2,7 @@
 uid: np2e_bno055
 title: NeuropixelsV2e Bno055
 hardware: NeuropixelsV2e Headstage
-device: true
 bno055: true
+bnoOperator: PolledBno055Data
 hardwareOperator: NeuropixelsV2eHeadstage
 ---

articles/hardware/np2e/configuration.md

@@ -21,8 +21,10 @@ Default values for the headstage are:
     - This is also known as the **Shank 0 Bank A** `Channel Preset`
 - Setting the `Reference` to *External*
 
-> [!WARNING]
+> [!IMPORTANT]
 > The workflow will not run unless gain correction files are provided. Click the `NeuropixelsV2eHeadstage` operator, expand `NeuropixelsV2e` in the property pane, then choose the appropriate files by selecting either `GainCalibrationFileA` or `GainCalibrationFileB` and clicking the <kbd>...</kbd> button. If only one probe is plugged in, only one file is required.
 
 > [!TIP]
 > For additional details on how to manually configure the headstage, such as enabling specific electrodes for recording, or modify AP / LFP gain, check out the <xref:np2e_gui> page.
+
+[!INCLUDE [timestamp-info](../../../includes/configuration-timestamp.md)]

articles/hardware/np2e/npv2e.md

@@ -2,7 +2,6 @@
 uid: np2e_npv2e
 title: NeuropixelsV2e
 hardware: NeuropixelsV2e Headstage
-device: true
 ---
 
 > [!NOTE]

articles/hardware/np2e/overview.md

@@ -10,14 +10,15 @@ These are the devices available on the NeuropixelsV2e Headstage:
     - 1280 electrodes low-impedance TiN electrodes per shank (5120 total for quad-shank probes).
     - 384 parallel, full-band (AP, LFP), low-noise recording channels.
         - Bandwidth of 0.3-10 kHz, sampled at 30 kHz
-- [Bno055](xref:np2e_bno055): 9-axis IMU for real-time, 3D orientation tracking and easy automated commutation with Open Ephys commutators.
+- [Bno055](xref:np2e_bno055): 9-axis IMU for real-time, 3D orientation tracking sampled up to ~100 Hz for easy automated commutation with Open Ephys commutators.
 
 > [!TIP]
 > Visit the [NeuropixelsV2e Headstage Hardware Guide](https://open-ephys.github.io/onix-docs/Hardware%20Guide/Headstages/headstage-neuropix-2e.html) to learn more about the hardware such as weight, dimensions, and proper power voltages.
 
 The example workflow below can by copy/pasted into the Bonsai editor using the clipboard icon in the top right. This workflow:
-- Captures data from the Bno055 IMU and Neuropixels 2.0 probe(s) and streams it to disk.
-- Monitors the the NeuropixelsV2e Headstage port status
+- Captures electrophysiology data from the Neuropixels 2.0 probe(s) and saves it to disk.
+- Captures orientation data from the Bno055 IMU and saves it to disk.
+- Monitors the NeuropixelsV2e Headstage port status
 - Automatically commutates the tether if there is a proper commutator connection. 
 
 ::: workflow
@@ -28,6 +29,3 @@ The following pages in the NeuropixelsV2e Headstage Guide provide a breakdown of
 
 > [!NOTE]
 > The NeuropixelsV2eBeta Headstage example workflow (<a href="~/workflows/hardware/np2ebeta.bonsai" download>download here</a>) is nearly identical to the NeuropixelsV2e Headstage example workflow. Follow the pages in the NeuropixelsV2e Headstage Guide to learn how it works.
-
-> [!TIP]
-> Visit the <xref:getting-started> pages if you are unfamiliar with using ONIX hardware in Bonsai.