Skip to content

Commit

Permalink
Add NeuropixelsV1e GUI page
Browse files Browse the repository at this point in the history
- Edited text copied from v2e gui page to be relevant for v1e
- Add all NeuropixelsV1e GUI images
- Finish adding new content
  • Loading branch information
bparks13 committed Sep 27, 2024
1 parent c7c1a90 commit ac77c22
Show file tree
Hide file tree
Showing 40 changed files with 227 additions and 10 deletions.
217 changes: 217 additions & 0 deletions articles/hardware/np1e/gui.md

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion articles/hardware/np1e/overview.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.
16 changes: 8 additions & 8 deletions articles/hardware/np2e/gui.md
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ 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){width=700px}

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 button showing three dots (ellipsis) on the right-most part of the property pane (#1 above).

Expand All @@ -69,7 +69,7 @@ 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]
Expand All @@ -82,7 +82,7 @@ Once the file is selected, press `Open` or <kbd>Enter</kbd>. This will populate
### 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).
Expand All @@ -92,7 +92,7 @@ Underneath the probe calibration filepath, there is a dropdown menu for choosing
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:
Expand Down Expand Up @@ -139,8 +139,8 @@ To select, as described [above](#maneuvering-along-the-probe), either click-and-
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>

Expand All @@ -149,7 +149,7 @@ The short video below shows how to select, clear selection, enable selected elec
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
Expand All @@ -173,7 +173,7 @@ 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).

Expand Down
2 changes: 1 addition & 1 deletion articles/toc.yml
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -55,4 +56,3 @@
- name: Bno055 & Commutation
href: hardware/np2e/bno055.md
- href: hardware/np2e/gui.md

Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
Binary file not shown.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file added img-src/neuropixelsv1e-gui/headstage-bno055.xcf
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.

0 comments on commit ac77c22

Please sign in to comment.