From d5ed1fc7f785fc7c5e753dc50799fa9b88e0fe1b Mon Sep 17 00:00:00 2001
From: bparks13 <bap@open-ephys.org>
Date: Fri, 18 Jul 2025 15:07:50 -0400
Subject: [PATCH 1/2] Add 2D arrays to correctly track both Neuropixels 2e
 probes

---
 Source/Devices/Neuropixels2e.cpp | 25 +++++++++++++------------
 Source/Devices/Neuropixels2e.h   | 12 ++++++------
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/Source/Devices/Neuropixels2e.cpp b/Source/Devices/Neuropixels2e.cpp
index d3a04d7..99a5eac 100644
--- a/Source/Devices/Neuropixels2e.cpp
+++ b/Source/Devices/Neuropixels2e.cpp
@@ -30,14 +30,16 @@ Neuropixels2e::Neuropixels2e(std::string name, std::string hubName, const oni_de
 	INeuropixel(NeuropixelsV2eValues::numberOfSettings, NeuropixelsV2eValues::numberOfShanks)
 {
 	probeSN.fill(0);
+  frameCount.fill(0);
+  sampleNumber.fill(0);
 
 	for (int i = 0; i < NeuropixelsV2eValues::numberOfSettings; i++)
 	{
 		defineMetadata(settings[i].get(), NeuropixelsV2eValues::numberOfShanks);
 	}
 
-	for (int i = 0; i < numFrames; i++)
-		eventCodes[i] = 0;
+	for (int i = 0; i < NumberOfProbes; i++)
+		eventCodes[i].fill(0);
 }
 
 Neuropixels2e::~Neuropixels2e()
@@ -495,8 +497,8 @@ uint64_t Neuropixels2e::getProbeSN(uint8_t probeSelect)
 
 void Neuropixels2e::startAcquisition()
 {
-	sampleNumber = 0;
-	frameCount = 0;
+  frameCount.fill(0);
+  sampleNumber.fill(0);
 }
 
 void Neuropixels2e::stopAcquisition()
@@ -535,8 +537,8 @@ void Neuropixels2e::processFrames()
 		uint16_t probeIndex = *(dataPtr + 4);
 		uint16_t* amplifierData = dataPtr + 9;
 
-		sampleNumbers[frameCount] = sampleNumber;
-		timestamps[frameCount] = deviceContext->convertTimestampToSeconds(frame->time);
+		sampleNumbers[probeIndex][frameCount[probeIndex]] = sampleNumber[probeIndex]++;
+		timestamps[probeIndex][frameCount[probeIndex]] = deviceContext->convertTimestampToSeconds(frame->time);
 
 		for (int i = 0; i < FramesPerSuperFrame; i++)
 		{
@@ -546,18 +548,17 @@ void Neuropixels2e::processFrames()
 			{
 				const size_t channelIndex = rawToChannel[j][i];
 
-				samples[channelIndex * numFrames + frameCount] =
+				samples[probeIndex][channelIndex * numFrames + frameCount[probeIndex]] =
 					(float)(*(amplifierData + adcIndices[j] + adcDataOffset)) * gainCorrection[probeIndex];
 			}
 		}
 
-		frameCount++;
-		sampleNumber++;
+		frameCount[probeIndex]++;
 
-		if (frameCount >= numFrames)
+		if (frameCount[probeIndex] >= numFrames)
 		{
-			amplifierBuffer[probeIndex]->addToBuffer(samples.data(), sampleNumbers, timestamps, eventCodes, numFrames);
-			frameCount = 0;
+			amplifierBuffer[probeIndex]->addToBuffer(samples[probeIndex].data(), sampleNumbers[probeIndex].data(), timestamps[probeIndex].data(), eventCodes[probeIndex].data(), numFrames);
+			frameCount[probeIndex] = 0;
 		}
 
 		oni_destroy_frame(frame);
diff --git a/Source/Devices/Neuropixels2e.h b/Source/Devices/Neuropixels2e.h
index ff0d039..955165f 100644
--- a/Source/Devices/Neuropixels2e.h
+++ b/Source/Devices/Neuropixels2e.h
@@ -124,14 +124,14 @@ namespace OnixSourcePlugin
 		static const int numFrames = 10;
 		static const int numSamples = numberOfChannels * numFrames;
 
-		std::array<float, numSamples> samples;
+		std::array<std::array<float, numSamples>, NumberOfProbes> samples {};
 
-		int64 sampleNumbers[numFrames];
-		double timestamps[numFrames];
-		uint64 eventCodes[numFrames];
+		std::array<std::array<int64_t, numFrames>, NumberOfProbes> sampleNumbers {};
+		std::array<std::array<double, numFrames>, NumberOfProbes> timestamps {};
+		std::array<std::array<uint64_t, numFrames>, NumberOfProbes> eventCodes {};
 
-		int frameCount = 0;
-		int sampleNumber = 0;
+		std::array<int, NumberOfProbes> frameCount;
+		std::array<int64_t, NumberOfProbes> sampleNumber;
 
 		std::unique_ptr<I2CRegisterContext> serializer;
 		std::unique_ptr<I2CRegisterContext> deserializer;

From 6883d39ec56fd2fa16f47d7048fbda999bcc7500 Mon Sep 17 00:00:00 2001
From: bparks13 <bap@open-ephys.org>
Date: Mon, 21 Jul 2025 09:56:26 -0400
Subject: [PATCH 2/2] Remove unsigned integer offset in Neuropixels 2.0 probes

---
 Source/Devices/Neuropixels2e.cpp | 2 +-
 Source/Devices/Neuropixels2e.h   | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/Source/Devices/Neuropixels2e.cpp b/Source/Devices/Neuropixels2e.cpp
index 99a5eac..6452606 100644
--- a/Source/Devices/Neuropixels2e.cpp
+++ b/Source/Devices/Neuropixels2e.cpp
@@ -549,7 +549,7 @@ void Neuropixels2e::processFrames()
 				const size_t channelIndex = rawToChannel[j][i];
 
 				samples[probeIndex][channelIndex * numFrames + frameCount[probeIndex]] =
-					(float)(*(amplifierData + adcIndices[j] + adcDataOffset)) * gainCorrection[probeIndex];
+					(float)(*(amplifierData + adcIndices[j] + adcDataOffset)) * gainCorrection[probeIndex] + DataMidpoint;
 			}
 		}
 
diff --git a/Source/Devices/Neuropixels2e.h b/Source/Devices/Neuropixels2e.h
index 955165f..00682a5 100644
--- a/Source/Devices/Neuropixels2e.h
+++ b/Source/Devices/Neuropixels2e.h
@@ -95,6 +95,9 @@ namespace OnixSourcePlugin
 
 		static constexpr int NumberOfProbes = 2;
 
+		static constexpr uint16_t NumberOfAdcBins = 4096;
+		static constexpr float DataMidpoint = NumberOfAdcBins / 2;
+
 		DataBuffer* amplifierBuffer[NumberOfProbes];
 
 		std::array<uint64_t, NumberOfProbes> probeSN;