Synchronization

1.0 or 2.0 probes recorded with a PXIe-based system

You have two options:

• configure the IMEC card(s) to output a sync signal. These sync pulses can only be generated at regular intervals (1 or 10Hz), which can sometimes make synchronization tricky.

• use a separate device to generate a sync signal, that is then sent as input to the IMEC card(s) in the chassis. The best practice is to generate these at pseudo-random intervals, making it easy to synchronize data.

Here is some code to implement this with an arduino:

const int poissonPin = 7;
const int minPoissonDur = 10; //ms
const int maxPoissonDur = 200; //ms

int currentPoissonState = 0;

void setup() {
  // put your setup code here, to run once:

  pinMode(poissonPin, OUTPUT);
  digitalWrite(poissonPin, LOW);
  currentPoissonState = LOW;
}

void loop() {
  // put your main code here, to run repeatedly:

  //code for flipper
  int poissonStateDur = random(minPoissonDur, maxPoissonDur);
  delay(poissonStateDur);
  if (currentPoissonState==LOW){
    currentPoissonState=HIGH;
  } 
  else {
    currentPoissonState=LOW;
  }
  digitalWrite(poissonPin, currentPoissonState);
  
}

More details and resources on synchronization can be found here.

1.0 or Phase3A probes recorded with an FPGA-based system.

Synchronizing other signals with electrophysiological data from Neuropixels probes can be achieved by providing up to 16 signals of your choice to the basestation. These signals will be treated as digital TTL inputs and their value (high or low) will be recorded alongside the electrophysiological data stream.

Note that the FPGA boards have independent clocks, so if you are using more than one Neuropixels probe simultaneously, you should take care to ensure that they are each synchronized appropriately, since they will drift relative to each other.

You can connect to all the digital input pins at once using a 24-way IDC connector, like this one or connect to an individual pin with a female d-sub crimp connector like this one.