Skip to content

Add support for single-shank Neuropixels 2.0 probes #493

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 4 commits into
base: main
Choose a base branch
from
Draft

Add support for single-shank Neuropixels 2.0 probes #493

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
51bf2cc
Add support for single-shank Neuropixels 2.0 probes
bparks13 Sep 8, 2025
dcb09c1
Disable the probe type dropdown for beta probes
bparks13 Sep 23, 2025
0f71eaa
Ensure that the correct probe group is loaded
bparks13 Sep 24, 2025
bcaadbc
Save probe configurations for both probe types
bparks13 Sep 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
41 changes: 32 additions & 9 deletions OpenEphys.Onix1.Design/ChannelConfigurationDialog.cs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,11 +18,21 @@ public abstract partial class ChannelConfigurationDialog : Form
{
internal event EventHandler OnResizeZedGraph;

internal ProbeGroup ProbeGroup;
ProbeGroup probeGroup;

internal ProbeGroup ProbeGroup
{
get => probeGroup;
set
{
probeGroup = value;
SelectedContacts = new bool[probeGroup.NumberOfContacts];
}
}

internal readonly List<int> ReferenceContacts = new();

internal readonly bool[] SelectedContacts = null;
internal bool[] SelectedContacts { get; private set; } = null;

/// <summary>
/// Constructs the dialog window using the given probe group, and plots all contacts after loading.
Expand All @@ -42,8 +52,6 @@ public ChannelConfigurationDialog(ProbeGroup probeGroup)
ProbeGroup = probeGroup;
}

SelectedContacts = new bool[ProbeGroup.NumberOfContacts];

ReferenceContacts = new List<int>();

zedGraphChannels.MouseDownEvent += MouseDownEvent;
Expand Down Expand Up @@ -432,13 +440,25 @@ internal virtual bool OpenFile<T>() where T : ProbeGroup
return false;
}

if (ProbeGroup.NumberOfContacts == newConfiguration.NumberOfContacts)
bool skipContactNumberMismatchCheck = false;

if (ProbeGroup.Probes.First().Annotations.Name != newConfiguration.Probes.First().Annotations.Name)
{
var result = MessageBox.Show($"There is a mismatch between the current probe type ({ProbeGroup.Probes.First().Annotations.Name})" +
$" and the new probe type ({newConfiguration.Probes.First().Annotations.Name}). Continue loading?", "Probe Type Mismatch", MessageBoxButtons.YesNo);

if (result == DialogResult.No)
return false;

skipContactNumberMismatchCheck = true; // NB: If the probe names do not match, skip the check to see if the number of contacts match.
// Example: loading a Neuropixels single-shank 2.0 probe, but the current probe is a quad-shank 2.0 probe.
}

if (skipContactNumberMismatchCheck || ProbeGroup.NumberOfContacts == newConfiguration.NumberOfContacts)
{
newConfiguration.Validate();

ProbeGroup = newConfiguration;
DrawProbeGroup();
RefreshZedGraph();

return true;
}
Expand Down Expand Up @@ -1075,6 +1095,8 @@ private void MenuItemOpenFile(object sender, EventArgs e)
if (OpenFile<ProbeGroup>())
{
DrawProbeGroup();
ResetZoom();
UpdateFontSize();
RefreshZedGraph();
}
}
Expand All @@ -1083,6 +1105,7 @@ private void MenuItemLoadDefaultConfig(object sender, EventArgs e)
{
LoadDefaultChannelLayout();
DrawProbeGroup();
ResetZoom();
UpdateFontSize();
RefreshZedGraph();
}
Expand Down Expand Up @@ -1342,8 +1365,8 @@ internal static bool HasContactAnnotations(ProbeGroup probeGroup)
{
foreach (var probe in probeGroup.Probes)
{
if (probe.ContactAnnotations != null
&& probe.ContactAnnotations.Annotations != null
if (probe.ContactAnnotations != null
&& probe.ContactAnnotations.Annotations != null
&& probe.ContactAnnotations.Annotations.Length > 0)
{
return true;
Expand Down
30 changes: 15 additions & 15 deletions OpenEphys.Onix1.Design/NeuropixelsV2eChannelConfigurationDialog.cs
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,4 @@
using System;
using System.Collections.Generic;
using System.Drawing;
using System.Linq;
using System.Windows.Forms;
Expand All @@ -17,24 +16,24 @@ public partial class NeuropixelsV2eChannelConfigurationDialog : ChannelConfigura
internal event EventHandler OnFileLoad;

/// <summary>
/// Public <see cref="NeuropixelsV2QuadShankProbeConfiguration"/> object that is manipulated by
/// Public <see cref="NeuropixelsV2ProbeConfiguration"/> object that is manipulated by
/// <see cref="NeuropixelsV2eChannelConfigurationDialog"/>.
/// </summary>
public NeuropixelsV2QuadShankProbeConfiguration ProbeConfiguration;
public NeuropixelsV2ProbeConfiguration ProbeConfiguration;

/// <summary>
/// Initializes a new instance of <see cref="NeuropixelsV2eChannelConfigurationDialog"/>.
/// </summary>
/// <param name="probeConfiguration">A <see cref="NeuropixelsV2QuadShankProbeConfiguration"/> object holding the current configuration settings.</param>
public NeuropixelsV2eChannelConfigurationDialog(NeuropixelsV2QuadShankProbeConfiguration probeConfiguration)
/// <param name="probeConfiguration">A <see cref="NeuropixelsV2ProbeConfiguration"/> object holding the current configuration settings.</param>
public NeuropixelsV2eChannelConfigurationDialog(NeuropixelsV2ProbeConfiguration probeConfiguration)
: base(probeConfiguration.ProbeGroup)
{
zedGraphChannels.ZoomButtons = MouseButtons.None;
zedGraphChannels.ZoomButtons2 = MouseButtons.None;

zedGraphChannels.ZoomStepFraction = 0.5;

ProbeConfiguration = probeConfiguration;
ProbeConfiguration = new(probeConfiguration);

ZoomInBoundaryX = 600;
ZoomInBoundaryY = 600;
Expand All @@ -46,13 +45,16 @@ public NeuropixelsV2eChannelConfigurationDialog(NeuropixelsV2QuadShankProbeConfi

internal override ProbeGroup DefaultChannelLayout()
{
return new NeuropixelsV2eProbeGroup();
return new NeuropixelsV2eProbeGroup(ProbeConfiguration.ProbeType);
}

internal override void LoadDefaultChannelLayout()
{
ProbeConfiguration = new(ProbeConfiguration.Probe, ProbeConfiguration.Reference);
ProbeGroup = ProbeConfiguration.ProbeGroup;
base.LoadDefaultChannelLayout();
ProbeConfiguration = new((NeuropixelsV2eProbeGroup)ProbeGroup,
ProbeConfiguration.Probe,
ProbeConfiguration.ProbeType,
ProbeConfiguration.Reference);

OnFileOpenHandler();
}
Expand All @@ -61,8 +63,6 @@ internal override bool OpenFile<T>()
{
if (base.OpenFile<NeuropixelsV2eProbeGroup>())
{
ProbeConfiguration = new((NeuropixelsV2eProbeGroup)ProbeGroup, ProbeConfiguration.Reference, ProbeConfiguration.Probe);

OnFileOpenHandler();

return true;
Expand Down Expand Up @@ -173,7 +173,7 @@ internal override void DrawScale()

const float scaleBarWidth = 1;

curve.Line.Width = scaleBarWidth;
curve.Line.Width = scaleBarWidth;
curve.Label.IsVisible = false;
curve.Symbol.IsVisible = false;
curve.Tag = ScalePointsTag;
Expand All @@ -197,7 +197,7 @@ internal override void HighlightEnabledContacts()
var contactsToEnable = contactObjects.Where(c =>
{
var tag = c.Tag as ContactTag;
var channel = NeuropixelsV2QuadShankElectrode.GetChannelNumber(tag.ContactIndex);
var channel = NeuropixelsV2Electrode.GetChannelNumber(tag.ContactIndex, ProbeConfiguration.ProbeType);
return ProbeConfiguration.ChannelMap[channel].Index == tag.ContactIndex;
});

Expand Down Expand Up @@ -227,7 +227,7 @@ internal override void UpdateContactLabels()
textObjsToUpdate = textObjs.Where(c =>
{
var tag = c.Tag as ContactTag;
var channel = NeuropixelsV2QuadShankElectrode.GetChannelNumber(tag.ContactIndex);
var channel = NeuropixelsV2Electrode.GetChannelNumber(tag.ContactIndex, ProbeConfiguration.ProbeType);
return ProbeConfiguration.ChannelMap[channel].Index == tag.ContactIndex;
});

Expand All @@ -242,7 +242,7 @@ internal override string ContactString(int deviceChannelIndex, int index)
return index.ToString();
}

internal void EnableElectrodes(NeuropixelsV2QuadShankElectrode[] electrodes)
internal void EnableElectrodes(NeuropixelsV2Electrode[] electrodes)
{
ProbeConfiguration.SelectElectrodes(electrodes);
}
Expand Down
7 changes: 5 additions & 2 deletions OpenEphys.Onix1.Design/NeuropixelsV2eDialog.cs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,11 @@ public NeuropixelsV2eDialog(IConfigureNeuropixelsV2 configureNode)
InitializeComponent();
Shown += FormShown;

bool isBeta = false;

if (configureNode is ConfigureNeuropixelsV2eBeta configureV2eBeta)
{
isBeta = true;
ConfigureNode = new ConfigureNeuropixelsV2eBeta(configureV2eBeta);
Text = Text.Replace("NeuropixelsV2e ", "NeuropixelsV2eBeta ");
}
Expand All @@ -38,15 +41,15 @@ public NeuropixelsV2eDialog(IConfigureNeuropixelsV2 configureNode)

ProbeConfigurations = new List<NeuropixelsV2eProbeConfigurationDialog>
{
new(ConfigureNode.ProbeConfigurationA, ConfigureNode.GainCalibrationFileA, ConfigureNode.InvertPolarity)
new(ConfigureNode.ProbeConfigurationA, ConfigureNode.GainCalibrationFileA, ConfigureNode.InvertPolarity, isBeta)
{
TopLevel = false,
FormBorderStyle = FormBorderStyle.None,
Dock = DockStyle.Fill,
Parent = this,
Tag = NeuropixelsV2Probe.ProbeA
},
new(ConfigureNode.ProbeConfigurationB, ConfigureNode.GainCalibrationFileB, ConfigureNode.InvertPolarity)
new(ConfigureNode.ProbeConfigurationB, ConfigureNode.GainCalibrationFileB, ConfigureNode.InvertPolarity, isBeta)
{
TopLevel = false,
FormBorderStyle = FormBorderStyle.None,
Expand Down
Loading
Loading