Add Neuropixels headstage tutorials

articles/getting-started/index.md

@@ -8,8 +8,5 @@ and Bonsai, and will teach them what ONIX is, how to download and install Bonsai
 place operators (and understand what an operator is), reorder a workflow, run a workflow, and
 finally visualize data.
 
-For those who are already familiar with Bonsai and are looking for a particular device or headstage
-to learn more about the hardware and how to utilize it, the table of contents on the left contains
-entries for each available device and headstage. Choose a page to learn more about the hardware and
-view a fully complete workflow that can be copied directly into Bonsai to aid in quickly setting up
-and collecting data from a system.
+For those who are already familiar with Bonsai and ONIX and are looking for a particular device or headstage
+to learn about and how to utilize, visit the <xref:hardware>.

articles/hardware/index.md

@@ -3,4 +3,4 @@ uid: hardware
 title: Hardware Guides
 ---
 
-Here you will find user guides for the ONIX breakout board, headstages, and other compatible hardware that are supported by the library.
+Here you will find user guides for the ONIX breakout board, headstages, and other compatible hardware that are supported by the library.

articles/hardware/np1e/bno055.md

@@ -0,0 +1,8 @@
+---
+uid: np1e_bno055
+title: NeuropixelsV1e Bno055
+hardware: NeuropixelsV1e Headstage
+device: true
+bno055: true
+hardwareOperator: NeuropixelsV1eHeadstage
+---

articles/hardware/np1e/configuration.md

@@ -0,0 +1,28 @@
+---
+uid: np1e_configuration
+title: Neuropixels 1.0 Headstage Configuration
+hardware: NeuropixelsV1e Headstage
+configuration: true
+operator: ConfigureNeuropixelsV1eHeadstage
+dataRate: 20.6
+timeUntilFullBuffer: 200 μs
+blockReadSize: 4096
+workflowLocation: overview
+---
+
+## 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:
+- Enabling the first 384 electrodes for streaming (electrodes 0 through 383)
+    - This is also known as the **Bank A** `Channel Preset`
+- Setting `AP Gain` to 1000x
+- Setting `LFP gain` to 50x
+- Enabling the `Spike Filter`
+- Setting the `Reference` to *External*
+
+> [!WARNING]
+> The workflow will not run unless gain calibration and ADC calibration files are provided. Click the `NeuropixelsV1eHeadstage` operator, expand `NeuropixelsV1e` in the property 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.

articles/hardware/np1e/npv1e.md

@@ -0,0 +1,22 @@
+---
+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.
+
+::: workflow
+![/workflows/hardware/breakout/np1.bonsai workflow](../../../workflows/hardware/np1e/np1.bonsai)
+:::
+
+The <xref:OpenEphys.Onix1.NeuropixelsV1eData> operator generates a sequence of <xref:OpenEphys.Onix1.NeuropixelsV1eDataFrame>s using the following settings:
+- `BufferSize` is set to 36.
+- The `NeuropixelsV1eData`'s `DeviceName` property is set to "NeuropixelsV1eHeadstage/NeuropixelsV1e". This links the <xref:OpenEphys.Onix1.NeuropixelsV1eData> operator to the corresponding configuration operator.
+
+Given the settings above, each frame will contain a [1 x 36 sample] `Clock` vector, a [384 channel x
+  36 sample] `SpikeData` matrix, and a [384 channel x 3 sample] `LfpData` matrix. This corresponds to 1.2 ms of data per data frame.
+  `LfpData` has less samples than `Clock` and `SpikeData` because `LfpData` is sampled at a lower rate; AP data is sampled at 30 kHz while LFP data is sampled at 2.5 kHz.
+
+The relevant properties are extracted from the <xref:OpenEphys.Onix1.NeuropixelsV1eDataFrame> by right-clicking the <xref:OpenEphys.Onix1.NeuropixelsV1eData> operator, and choosing the following **Output** members: `Clock`, `SpikeData`, and `LfpData`. The [`MatrixWriter`](https://bonsai-rx.org/docs/api/Bonsai.Dsp.MatrixWriter.html) operators saves the selected members to files with the following format: `np1-clock_<timestamp>.raw`, `np1-spike_<timestamp>.raw`, and `np1-lfp_<timestamp>.raw`, respectively.

articles/hardware/np1e/overview.md

@@ -0,0 +1,31 @@
+---
+uid: np1e_npv1e-headstage
+title: NeuropixelsV1e Headstage
+---
+
+These are the devices available on the NeuropixelsV1e Headstage:
+
+- One [NeuropixelsV1e](xref:np1e_npv1e):
+    - A single 1cm long shank probe with a 70 x 24 µm shank cross-section.
+    - 960-electrode low-impedance TiN electrodes total.
+    - 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.
+
+> [!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.
+- 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

@@ -0,0 +1,8 @@
+---
+uid: np1e_port-status
+title: Port Status
+hardware: NeuropixelsV1e Headstage
+device: true
+portStatus: true
+hardwareOperator: NeuropixelsV1eHeadstage
+---

articles/hardware/np2e/bno055.md

@@ -0,0 +1,8 @@
+---
+uid: np2e_bno055
+title: NeuropixelsV2e Bno055
+hardware: NeuropixelsV2e Headstage
+device: true
+bno055: true
+hardwareOperator: NeuropixelsV2eHeadstage
+---

articles/hardware/np2e/configuration.md

@@ -0,0 +1,28 @@
+---
+uid: np2e_configuration
+title: NeuropixelsV2e Headstage Configuration
+hardware: NeuropixelsV2e Headstage
+configuration: true
+operator: ConfigureNeuropixelsV2eHeadstage
+dataRate: 18.1
+timeUntilFullBuffer: 220 μs
+blockReadSize: 4096
+workflowLocation: overview
+---
+
+> [!NOTE]
+> The NeuropixelsV2eBeta Headstage functions nearly identically to the NeuropixelsV2e Headstage. Simply replace `ConfigureNeuropixelsV2eHeadstage` with `ConfigureNeuropixelsV2eBetaHeadstage`.
+
+## Configuring the NeuropixelsV2e headstage
+The `NeuropixelsV2eHeadstage` operator is set to configure the NeuropixelsV2e Headstage; this can enable streaming of electrophysiology data from a Neuropixels 2.0 probe and orientation data from a Bno055 IMU. This is accomplished in the NeuropixelsV2e Headstage example workflow by leaving all of the `NeuropixelsV2eHeadstage` properties set to their default values.
+
+Default values for the headstage are:
+- Enabling the first 384 electrodes of the first shank for streaming (shank 0, electrodes 0 through 383)
+    - This is also known as the **Shank 0 Bank A** `Channel Preset`
+- Setting the `Reference` to *External*
+
+> [!WARNING]
+> 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.