Equipment_List

Neuropixels 1.0 and 2.0 probes equipment [which version do I have? ]

1.0 probes (on sale now) require different cables and headstages than Phase3A, and are used with a new PXIe-based system. See https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/SystemRequirements_PXI.md and neuropixels.org for more information. A limited number of FPGA-based recording systems for P3B were developed for testing but these are not generally available.

2.0 probes additionally require different headstages (that can get input from up to 2 probes) than 1.0, but use the same cables.

To record data from a Neuropixels 1.0 and 2.0 probes, you will need:

• Headstage (IMEC-supplied, different for 1.0 and 2.0 probes)
• Cable (IMEC-supplied)
• PXIe chassis (eg PXIe-1071)
• IMEC card (IMEC-supplied - maximum 2 per chassis, allowing the simultaneous recording to 8 1.0 probes or 16 2.0 probes)
• PXIe module (eg PXIe-8381)
• PCIe card (eg PCIe-8381)
• Acquisition computer with:
  • Minimum 6 cores (Passmark rating > 13000)
  • Minimum 3.5 GHz
  • Minimum 16GB memory
  • Graphics Card: Nvidia GeForce 1060 or better
  • Dedicated data drive (SSD or NVMe, 500+ MB/s)
  • PCIe 8X slot for the PXIe controller
• Optionally, to align signals between probes and with other computers, you can add a separate device, such as an Arduino, to generate a sync signal that is inputed to the IMEC card(s) in the chassis and to any NIDAQ or similar device (see the section below).

here is a schematic of an example rig:

1.0 and 2.0 probes - aligning

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 aligning 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 bext parctice is to generate these at pseudo-random intervals, making it easy to align 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 aligning can be found here.

Phase3A probes [which version do I have? ]

To record data from a Neuropixels Phase3A probe, you will need:

• Headstage (IMEC-supplied)
• Cable (IMEC-supplied)
• Basestation (IMEC-supplied)
• FPGA: Xilinx Kintex-7 KC705. E.g. from Digikey
• Acquisition computer
  • Required: gigabit ethernet port
  • Recommended: good GPU, SSD hard drive (not the same drive the OS is on)

An example rig (old FPGA-based system):

This is an example of a complete and working setup for an anesthetized recording.