Add NeuropixelsV1e GUI page (#78)

* Add NeuropixelsV1e GUI page
- Edited text copied from v2e gui page to be relevant for v1e
- Add all NeuropixelsV1e GUI images
- Finish adding new content

* Minor Edits

- Fixed xref that was missing the side carets <>
- Removed some commas that felt like they weren't necessary in my
  understanding of the english language
- Removed colons and unified GUI fields using back ticks ` instead of
  quotation marks "

* Added note
- Now this matches the NPX 2.0e GUI page

---------

Co-authored-by: cjsha <[email protected]>

articles/hardware/np1e/configuration.md

@@ -22,7 +22,7 @@ Default values for the headstage are:
 - 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.
+> 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.
+> 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/overview.md

@@ -28,4 +28,4 @@ The example workflow below can by copy/pasted into the Bonsai editor using the c
 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.
+> Visit the <xref:getting-started> pages if you are unfamiliar with Bonsai.

articles/hardware/np2e/gui.md

@@ -6,7 +6,7 @@ title: NeuropixelsV2e GUI
 > [!NOTE]
 > The Neuropixels V2e Beta Headstage GUI functions identically to the Neuropixels V2e Headstage. 
 
-In addition to the capabilities described in <xref:np2e>, the `NeuropixelsV2e` headstage has a graphical user interface when the `OpenEphys.Onix1.Design` package is downloaded. For more information on how to install that library, check out the <xref:install-configure-bonsai> page.
+The `NeuropixelsV2e` headstage has a graphical user interface when the `OpenEphys.Onix1.Design` package is downloaded. For more information on how to install that library, check out the <xref:install-configure-bonsai> page.
 
 ## Overview
 
@@ -38,7 +38,10 @@ In addition to the absolute number of channels, there are other restrictions in
 
 ### Keeping or discarding configuration settings
 
-While the GUI is open, any changes made to the configuration settings can be freely modified and will not affect the configuration unless `Okay` is pressed. This includes all aspects of the configuration, such as which electrodes are enabled, the chosen reference channel, and even the probe calibration file.
+While the GUI is open, any changes to the configuration settings can be freely modified and will not affect the configuration unless `Okay` is pressed. This includes all aspects of the configuration, such as which electrodes are enabled, the chosen reference channel, and the probe calibration file.
+
+> [!NOTE]
+> The hardware is not actually configured until the workflow starts.
 
 If the window is closed any other way (such as by pressing `Cancel`, or pressing the <kbd>X</kbd> to close the window), then any changes made *will not* be saved.
 
@@ -53,7 +56,7 @@ When opening the GUI, there is a default probe configuration that is loaded and
 ![Open the GUI](../../../images/neuropixelsv2e-gui-tut/bonsai-editor-where-to-click.png)
 
 Steps to open the Probe Configuration GUI:
-- Select the `NeuropixelsV2eHeadstage` node.
+- Select the `ConfigureNeuropixelsV2eHeadstage` node.
 - Click on the `NeuropixelsV2eProbeConfiguration` to edit (either `ProbeConfigurationA` or `ProbeConfigurationB`).
 - Select the <kbd>...</kbd> button on the right-most part of the property pane (#1 above).
 
@@ -69,30 +72,30 @@ Once opened, if no probe calibration file has been selected the window should lo
 Upon opening the GUI for the first time, if no probe calibration file was set in the Bonsai editor, the window will be mostly blank. To populate the window with a drawing of the probe, click on the ellipsis button to the right of the empty text box under "Probe Calibration File:" (see below). This will open a file dialog, where the calibration file can be searched for and selected. 
 
 <p align="center">
-  <img src="~/images/neuropixelsv2e-gui-tut/probeconfiguration-filecalibration.png">
+  <img src="../../../images/neuropixelsv2e-gui-tut/probeconfiguration-filecalibration.png">
 </p>
 
 > [!NOTE]
 > Files are expected to be named `XXXXXXXXXXX_gainCalValues.csv`, where "XXXXXXXXXXX" is the probe serial number.
 
-Once the file is selected, press `Open` or <kbd>Enter</kbd>. This will populate the text box with the filepath to the calibration file, and enable visualization of the electrodes. Below is a view of the Probe Configuration GUI that has been opened for `Probe A` with a gain calibration file selected. Note that the `Gain Correction` textbox and the `Gain Calibration SN: ` status strip are automatically filled in with values found in the calibration file.
+Once the file is selected, press `Open` or <kbd>Enter</kbd>. This will populate the text box with the filepath to the calibration file and enable visualization of the electrodes. Below is a view of the Probe Configuration GUI that has been opened for `Probe A` with a gain calibration file selected. Note that the `Gain Correction` textbox and the `Gain Calibration SN: ` status strip are automatically filled in with values found in the calibration file.
 
 ![Probe Configuration GUI with Probe shown](../../../images/neuropixelsv2e-gui-tut/probeconfiguration-dialog-with-probe.png)
 
 ### Selecting channel reference
 
 <p align="center">
-  <img src="~/images/neuropixelsv2e-gui-tut/probeconfiguration-reference.png">
+  <img src="../../../images/neuropixelsv2e-gui-tut/probeconfiguration-reference.png">
 </p>
 
 Underneath the probe calibration filepath, there is a dropdown menu for choosing the reference for all channels. For possible values and a brief description of what they correspond to, check out the [references page](xref:OpenEphys.Onix1.NeuropixelsV2QuadShankReference).
 
 ### Channel presets
 
-To save time, it is possible to select a preset channel combination from the `Channel Presets:` dropdown. These presets are defined to work within the constraints of `NeuropixelsV2e` channel combinations defined [above](#channel-constraints).
+To save time, it is possible to select a preset channel combination from the `Channel Presets` dropdown. These presets are defined to work within the constraints of `NeuropixelsV2e` channel combinations defined [above](#channel-constraints).
 
 <p align="center">
-  <img src="~/images/neuropixelsv2e-gui-tut/probeconfiguration-channelpresets.png">
+  <img src="../../../images/neuropixelsv2e-gui-tut/probeconfiguration-channelpresets.png">
 </p>
 
 Channel presets follow one of these patterns:
@@ -102,11 +105,11 @@ Channel presets follow one of these patterns:
 - All Shanks N_M
     - Enables all electrodes starting at shank index N up to shank index M across all four shanks
 
-If electrodes are manually enabled, the `Channel Presets:` dropdown will change to **None**, indicating that a channel preset is no longer selected.
+If electrodes are manually enabled, the `Channel Presets` dropdown will change to **None**, indicating that a channel preset is no longer selected.
 
 ### Maneuvering along the probe
 
-Once a GUI has been [opened](#open-probe-configuration-gui), and a probe calibration file has been [selected](#choosing-a-probe-calibration-file), the main panel on the left will be populated with a `NeuropixelsV2e` probe. Below are the buttons used to navigate within this panel to view and choose electrodes.
+Once a GUI has been [opened](#open-probe-configuration-gui) and a probe calibration file has been [selected](#choosing-a-probe-calibration-file), the main panel on the left will be populated with a `NeuropixelsV2e` probe. Below are the buttons used to navigate within this panel to view and choose electrodes.
 
 - Mouse Controls
     - Mouse wheel zooms in/out towards the cursor
@@ -136,20 +139,20 @@ Electrodes can be selected at any zoom level, but it is often preferable to zoom
 
 To select, as described [above](#maneuvering-along-the-probe), either click-and-drag the cursor over the desired electrodes, or select individual electrodes by clicking on them one-by-one. Once the electrodes to enable are selected, click on the `Enable Selected Electrodes` button in the right panel. At this point the selected electrodes should turn blue, indicating that they are now enabled. It is important to note that when electrodes are enabled, a number of previously enabled electrodes will be disabled due to channel constraints. For more information, read the [Channel constraints](#channel-constraints) section above.
 
-The short video below shows how to select, clear selection, enable selected electrodes, and translate using the scroll bar. Note that once electrodes are manually enabled, the `Channel Presets:` drop-down changes from `Shank0BankA` to `None`. Then, once the selected electrodes match the preset, it is automatically changed back to `Shank0BankA`.
+The short video below shows how to select, clear selection, enable selected electrodes, and translate using the scroll bar. Note that once electrodes are manually enabled, the `Channel Presets` drop-down changes from `Shank0BankA` to `None`. Then, once the selected electrodes match the preset, it is automatically changed back to `Shank0BankA`.
 
 <div>
-  <video width="650" height="365" controls autoplay muted loop>
-    <source src="~/images/neuropixelsv2e-gui-tut/probeconfiguration-enable-electrodes.webm">
+  <video width="650" height="365" controls muted loop>
+    <source src="../../../images/neuropixelsv2e-gui-tut/probeconfiguration-enable-electrodes.webm">
   </video>
 </div>
 
 ### Loading and saving channel configurations
 
-When the GUI is first opened, and after a probe calibration file has been specified, the default [ProbeInterface](#probeinterface) configuration is loaded and drawn in the main panel. In this case, the default configuration is for a quad-shank `NeuropixelsV2e` probe, with the `Shank0BankA` channel preset selected. To load a new configuration, load the default configuration, or save the current configuration, go to the File drop-down menu (see below) and choose the relevant option.
+When the GUI is first opened and after a probe calibration file has been specified, the default [ProbeInterface](#probeinterface) configuration is loaded and drawn in the main panel. In this case, the default configuration is for a quad-shank `NeuropixelsV2e` probe, with the `Shank0BankA` channel preset selected. To load a new configuration, load the default configuration, or save the current configuration, go to the File drop-down menu (see below) and choose the relevant option.
 
 <p align="center">
-  <img src="~/images/neuropixelsv2e-gui-tut/probeconfiguration-filemenu.png">
+  <img src="../../../images/neuropixelsv2e-gui-tut/probeconfiguration-filemenu.png">
 </p>
 
 #### Save ProbeInterface file
@@ -173,21 +176,21 @@ To load the default channel configuration at any time, navigate to the File drop
 
 Step to open the headstage configuration GUI
 
-  - Double-click the `NeuropixelsV2eHeadstage` node (#2 above)
+  - Double-click the `ConfigureNeuropixelsV2eHeadstage` node (#2 above)
 
 Once opened, if no probe calibration is selected for either `Probe A` or `Probe B`, then both tabs will only show their controls on the right and no probes (see below).
 
 ![Headstage Configuration GUI](../../../images/neuropixelsv2e-gui-tut/headstage-dialog.png)
 
 ### Configure Probe A
 
-Using the headstage configuration GUI is exactly the same as using the [probe configuration GUI](#open-probe-configuration-gui). After the GUI has been [opened](#open-headstage-configuration-gui), and a probe calibration file has been [selected](#choosing-a-probe-calibration-file), `Probe A` will be drawn in the corresponding tab (see below).
+Using the headstage configuration GUI is exactly the same as using the [probe configuration GUI](#open-probe-configuration-gui). After the GUI has been [opened](#open-headstage-configuration-gui) and a probe calibration file has been [selected](#choosing-a-probe-calibration-file), `Probe A` will be drawn in the corresponding tab (see below).
 
 ![Headstage Configuration GUI with probe A](../../../images/neuropixelsv2e-gui-tut/headstage-dialog-with-probe-a.png)
 
 ### Configure Probe B
 
-Using the headstage configuration GUI is exactly the same as using the [probe configuration GUI](#open-probe-configuration-gui). After the GUI has been [opened](#open-headstage-configuration-gui), and a probe calibration file has been [selected](#choosing-a-probe-calibration-file), `Probe B` will be drawn in the corresponding tab (see below).
+Using the headstage configuration GUI is exactly the same as using the [probe configuration GUI](#open-probe-configuration-gui). After the GUI has been [opened](#open-headstage-configuration-gui) and a probe calibration file has been [selected](#choosing-a-probe-calibration-file), `Probe B` will be drawn in the corresponding tab (see below).
 
 ![Headstage Configuration GUI with probe B](../../../images/neuropixelsv2e-gui-tut/headstage-dialog-with-probe-b.png)
 

articles/toc.yml

@@ -44,6 +44,7 @@
       href: hardware/np1e/npv1e.md
     - name: Bno055 & Commutation
       href: hardware/np1e/bno055.md
+    - href: hardware/np1e/gui.md
   - href: hardware/np2e/overview.md
     items: 
     - name: Configuration
@@ -55,4 +56,3 @@
     - name: Bno055 & Commutation
       href: hardware/np2e/bno055.md
     - href: hardware/np2e/gui.md 
-