OpenEphys.ProbeInterface.NET

A C# .NET library for reading and writing neural probe configurations in the probeinterface JSON format. Probeinterface is an open standard describing probe geometry, contact positions, and channel mappings, and is widely used by Open Ephys, SpikeInterface, and related tools.

What it does

• Deserializes probeinterface JSON files into strongly-typed .NET objects
• Serializes probe configurations back to compliant JSON
• Validates files against the specification on load (correct version format, required fields, unique channel indices, array length consistency)
• Supports all probe properties: contact positions (2D and 3D), shapes (circle, rect, square), plane axes, planar contour, shank IDs, contact sides, and free-form per-contact annotations with typed access

Quick start

using Newtonsoft.Json;
using OpenEphys.ProbeInterface.NET;

// Load a probeinterface JSON file
var json = File.ReadAllText("my_probe.json");
var probeGroup = JsonConvert.DeserializeObject<ProbeGroup>(json);

// Iterate contacts on each probe
foreach (var probe in probeGroup.Probes)
{
    foreach (var contact in probe.Contacts)
        Console.WriteLine($"Contact {contact.ContactId}: ({contact.PosX}, {contact.PosY})");
}

// Access per-contact annotations at the contact level
var probe0 = probeGroup.Probes.First();
var contact0 = probe0.Contacts[0];
double? impedance = contact0.GetAnnotation<double>("impedance");
string? region = contact0.GetAnnotation<string>("brain_area");

// Set or remove an annotation on a single contact
contact0.SetAnnotation("brain_area", "CA1");
contact0.RemoveAnnotation("brain_area");

// Bulk access across all contacts on a probe (returns one element per contact)
double[]? impedances = probe0.GetContactAnnotation<double>("impedance");
probe0.SetContactAnnotation("brain_area", new[] { "CA1", "CA3", "DG" });
probe0.RemoveContactAnnotation("brain_area");

// Access probe-level annotations (model, manufacturer, any custom fields)
Console.WriteLine(probe0.Annotations.ModelName);
probe0.Annotations.SetAnnotation("implant_date", "2025-01-01");
string? date = probe0.Annotations.GetAnnotation<string>("implant_date");

// Wire hardware channels to contacts (contact index → channel number)
// Validates uniqueness within and across all probes in the group
ChannelWiring.WireChannels(probeGroup, probeIndex: 0, new Dictionary<int, int>
{
    { 0, 3 }, { 1, 1 }, { 2, 2 }, { 3, 0 }
});

// Query the resulting channel map (channel number → probe/contact/Contact)
var map = probeGroup.GetChannelMap();
foreach (var (channel, entry) in map)
    Console.WriteLine($"Channel {channel} → probe {entry.ProbeIndex}, contact {entry.ContactIndex}");

// Wire a single contact, or clear the mapping when done
ChannelWiring.WireChannel(probeGroup, probeIndex: 0, contactIndex: 4, channel: 7);
ChannelWiring.UnwireChannel(probeGroup, probeIndex: 0, contactIndex: 4);
ChannelWiring.UnwireChannels(probeGroup, probeIndex: 0); // clear one probe
ChannelWiring.UnwireChannels(probeGroup); // clear all probes

// Serialize back to JSON
File.WriteAllText("output.json", JsonConvert.SerializeObject(probeGroup, Formatting.Indented));