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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
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‎api/configure.md

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title: Configuration Operators
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---
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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.
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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

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title: Device Configuration Operators
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---
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> [!CAUTION]
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> 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:
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> [!IMPORTANT]
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> 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:
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> - The `address` and `name` properties of aggregate configuration operators undergo automatic configuration which reduces the risk of erroneous configuration.
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> - 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.
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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.
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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

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

‎articles/hardware/breakout/memory-monitor.md

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---
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uid: breakout_memory-monitor
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title: Breakout Board Memory Monitor
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hardware: true
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device: memory monitor
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---
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‎articles/hardware/hs64/bno055.md

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---
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uid: hs64_bno055
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title: Headstage 64 Bno055
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hardware: Headstage 64
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bno055: true
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bnoOperator: Bno055Data
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hardwareOperator: Headstage 64
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---

‎articles/hardware/hs64/configuration.md

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---
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uid: hs64_configuration
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title: Headstage64 Configuration
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hardware: Headstage64
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configuration: true
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operator: ConfigureHeadstage64
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dataRate: 4.1
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timeUntilFullBuffer: 500 μs
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blockReadSize: 2048
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workflowLocation: workflow
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---
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## Configuring the Breakout Board and Headstage64
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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`.
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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.
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[!INCLUDE [timestamp-info](../../../includes/configuration-timestamp.md)]

‎articles/hardware/hs64/estim.md

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

‎articles/hardware/hs64/memory-monitor.md

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---
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uid: hs64_memory-monitor
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title: Headstage64 Memory Monitor
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---
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The following excerpt from the Breakout Board [example workflow](xref:breakout_workflow) demonstrates memory monitor functionality and saves memory monitor data.
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::: workflow
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![/workflows/hardware/breakout/memory-monitor.bonsai workflow](../../../workflows/hardware/breakout/memory-monitor.bonsai)
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:::
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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`.
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> [!NOTE]
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> The `MemoryMonitorDataFrame` operator generates a
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> data stream that is most useful in the context of closed-loop performance. It tells the user if data
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> is being consumed rapidly enough by the host PC to keep up with data production by the hardware. The
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> hardware FIFO is a buffer that is required to deal with the fact that computers with normal
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> operating systems cannot perform operations with strict regularity. When there are hiccups in
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> acquisition, the hardware FIFO picks up the slack, but should then be cleared immediately. To get
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> the lowest latencies, the `BlockReadSize` should be as small as possible *while the memory use
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> percentage remains around 0%*.
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> [!WARNING]
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> If the hardware FIFO's `PercentUsed` is non-zero for long time periods, or is increasing, the
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> `StartAcquisition`'s `BlockReadSize` setting is too small (see the [breakout board configuration](xref:breakout_configuration)). A small
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> `BlockReadSize` will mean that the host computer does not have to wait long for enough data to
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> become available to propagate it forward, but will reduce overall bandwidth by increasing the
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> frequency at which the host computer checks if data is available and performs hardware reads.

‎articles/hardware/hs64/ostim.md

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---
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uid: hs64_ostim
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title: Headstage 64 Optical Stimulation
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---
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The following excerpt from the Headstage64 [example workflow](xref:hs64_hs64) demonstrates optical stimulation.
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::: workflow
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![/workflows/hardware/hs64/ostim.bonsai workflow](../../../workflows/hardware/hs64/ostim.bonsai)
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:::
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‎articles/hardware/hs64/overview.md

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---
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uid: hs64_hs64
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title: Headstage 64
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---
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These are the devices available on the Headstage64:
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- [Rhd2164](xref:hs64_rhd2164):
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- 64 electrophysiology channels for passive probes (e.g. tetrode, silicon probe, etc.) sampled at 30 kHz with 16 bit depth
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- Adjustable analog band-pass filter:
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- Lower cutoff configurable from 0.1 Hz to 500 Hz
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- Upper cutoff configurable from 100 Hz to 20 kHz
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- Optional adjustable digital high-pass filter with cutoff configurable from 0.146 Hz to 3309 Hz
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- Three auxiliary ADC channels sampled at 30 kHz with 16 bit depth
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- [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
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- [Ts4231](xref:hs64_ts4231): For compatibility with HTC Vive Lighthouses for real-time, 3D position tracking
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- [Electrical Stimulation](xref:hs64_estim): Single current source with ±15V compliance voltage and automatic electrode discharge
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- The stimulation waveform is highly configurable via the <xref:OpenEphys.Onix1.Headstage64ElectricalStimulatorTrigger>'s properties.
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- [Optical Stimulation](xref:hs64_ostim): Two current sources with 800mA upper limit
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- The stimulation waveform is highly configurable via the <xref:OpenEphys.Onix1.Headstage64OpticalStimulatorTrigger>'s properties.
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> [!TIP]
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> For a detailed explanation of the Rhd2164 amplifier's properties, read the [datasheet](https://intantech.com/files/Intan_RHD2164_datasheet.pdf).
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> [!TIP]
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> 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.
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The following pages in the Headstage64 Guide provide an example workflow and a
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breakdown of its components.

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