What parts do I need for imec/Neuropixels experiments?
From Neuropixels.org, you need:
- Probe(s)
- Head stage(s)
- Cable(s)
- PXI base-station module(s)
You also need a PXI chassis setup:
- Chassis
- Controller module
- Controller PC card
- Controller link cable
You also probably want to collect non-neural data:
- PXI multifunction IO module
And you need a computer capable of running your system.
Computer requirements depend upon the number of probes and other signals to be acquired in an experiment. Heavy use of the visualization tools during acquisition are an additional burden. Since a single computer specification won't cover all uses of SpikeGLX, we give some rough guidelines and examples of systems we have tested.
This document also covers options for acquisition of non-neural data channels and what we know about different chassis options.
The following are what we think you should purchase if buying a new desktop machine for this application.
Up to 8 probes, plus NI channels:
- Windows 7 or 10, 64-bit
- NI Platform Services 18.5 or later
- NI-DAQmx 18.6 or later
- Minimum 6 cores (Passmark rating > 13000)
- Minimum 3.5 GHz
- Minimum 16GB memory
- Graphics Card: Nvidia GeForce 1060 or better (see, e.g. Passmark ratings for video cards)
- Dedicated data drive (SSD or NVMe, 500+ MB/s)
- PCIe 8X slot for the PXIe controller
Up to 16 probes, plus NI channels:
- Windows 7 or 10, 64-bit
- NI Platform Services 18.5 or later
- NI-DAQmx 18.6 or later
- Minimum 8 cores (Passmark rating > 18000)
- Minimum 3.5 GHz
- Minimum 32GB memory
- Graphics Card: Nvidia GeForce 1060 or better (see, e.g. Passmark ratings for video cards)
- Dedicated data drive (NVMe 2000+ MB/s write rate)
- PCIe 8X slot for the PXIe controller
Notes
- GeForce cards require PCs with 400W power supplies
- Google 'model_name passmark' (e.g. W-2145 passmark)
- The data drive should be distinct from the system drive
In SpikeGLX select menu item Window\Run Metrics to display a window
of performance measurements that provide some insight on whether the system
is running comfortably or struggling to keep up.
The following are systems we've tested in our lab. These are not recommendations (most of the hardware is no longer available); they are illustrations of working systems.
More work needs to be done to better understand which system attributes are the most significant.
Imec BS cards have no non-neural input channels, except for a single SMA connector that SpikeGLX uses to synchronize the card with other devices. However, SpikeGLX can record concurrently from the imec cards and from an additional multifunction or digital IO device to cover physiological data and trial marking signals. Neural and non-neural data are tightly synchronized.
SpikeGLX can actually operate two cards provided they have identical model numbers. We are treating such a pair as a single device with double the channel capacity.
SpikeGLX has these requirements for the non-neural device:
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It must be an NI device that we can talk to via DAQmx (a general purpose device programming language for NI hardware).
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It must be an M-series (62XX), S-series (61XX), X-series (63XX), or digital IO (653X) device.
Note: As of version 20190305 SpikeGLX can read up to 32 digital lines per device (previously limited to 8). Also, be aware that only a device's 'waveform' digital lines can be programmed for high sample rate input. You'll have to look at the device spec sheet to see the count of waveform lines. Digital device support is added as of version 20190413.
We have direct experience with these:
- PCI-based 6221 (M)
- PCI-based 6133 (S) (16 MS FIFO tested)
- PXI-based 6133 (S) (16 MS FIFO tested)
- PXI-based 6341 (X)
- PXI-based 6363 (X)
- USB-based 6366 (X)
- PXI-based 6535 (digital)
Some models (S and some X) have a feature called 'simultaneous sampling' which means each input channel gets its own amplifier and ADC. This allows the device to sample all its channels in parallel at the advertised maximum sample rate, for example, 2.5 mega-samples/s/channel for the 6133. Moreover, there is no crosstalk between the channels. That's what makes these models very capable and very expensive. This is a must when using a Whisper multiplexer which samples all AI channels at 800 kHz.
When doing multichannel acquisition, non-simultaneous-sampling devices,
such as the 6221, use a multiplexing scheme to connect inputs to the
single amplifier/ADC unit in quick succession. The fastest you can drive
such a device depends upon how many channels you want to sample. It's
R0/nChans, where, R0 is the advertised maximum sample rate, 250 KS/s for
the 6221. Be aware that switching from channel to channel at this rate
does not allow the amplifier to fully settle before the next input is
connected to it, hence, there will be some crosstalk (charge carryover).
To avoid that issue, one can run at a lower effective maximum sample
rate given by: 1/(1/R0 + 1E-5). For, the 6221 example, you should sample
no faster than 71428/nChans.
USB-based devices such as the 6366 can't use DMA data transfers, so have lower effective bandwidth and higher latency than PCI or PXI devices. Go ahead and use it if you already have one. However, don't use these for digital input channels: The combination of low transfer rates and a very small digital FIFO buffer make digital buffer overruns fairly common.
The X-series strike a balance between high sample rate (limited by settle time) and high channel count. The 6363 has 32 AI and 32 waveform DI channels. The 6341 has 32 single ended AI and 8 waveform DI channels for half the price. Remember that AI channels can equally well read analog and TTL inputs.
Your NI module will talk to the world via a high density multi-pin connector,
so you'll also want a breakout box (connector block) and cable that works
with your module. Browse here for
NI multifunction IO
devices. Click on a table entry and a View Accessories button will appear.
There are easier to use options like the BNC-2110 that provide BNCs for the
most often accessed channels, and the SCB-68A that offers only screw terminals
but is more versatile because you can access all channels.
BTW: Plural of chassis is also chassis.
We've successfully used these chassis with both imec BS modules and with an NI PXI-6133 multifunction IO module:
- NI 1082 (8 slots)
- NI 1071 (4 slots)
- ADLink PXES-2301 (6 slots)
What you need to know about the ADLink chassis is that it is very attractively priced and well made, but the PXI-6133 didn't work with this chassis right out of the box. That's because the routing of signals from one internal terminal to another over the chassis backplane is very slightly different. We got this to work fine, but it required some code rewrites to make it work. If you own or want to purchase other NI modules besides the 6133, then you might face some snags with this chassis. You should try to test it first.
We've tested these remote control modules (Chassis <-> PC) links:
- NI PXIe-8398 (16 GB/s)
- NI PXIe-8381 (4 GB/s)
- NI PXIe-8301 (2.3 GB/s Thunderbolt)
- ADLink 8638 (4 GB/s)
These mix and match in in our chassis without compatibility issues. At this time we can offer these additional remarks:
-
The 8398 may well be overkill. It did everything asked of it, up to 16 probes, which is the maximum we tested to, but it is very costly, uses up a PCI Gen 3 slot, and its thick cable is very unwieldy. In fact, the cable is heavy enough to worry that it might not hold securely in the device connectors which are somewhat flimsy.
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The 8381 and 8638 also performed perfectly in all tests out to 16 probes. This is what we recommend at present. They are more affordable, small, and need only Gen 2 slots.
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The Thunderbolt controller could only be tested in a laptop, which was quite capable for a laptop (the Thinkpad X1 in the table above), but we could only achieve stable performance up to 8 or perhaps 10 probes. We do not know if the laptop or the link is the limiting factor. More below.
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Having over a month of experience running with Thunderbolt we find that the link to the chassis tends to be dropped, and, the enclustra drivers are no longer recognized, after about 6 hours. That seems to be the case whether the machine is idle or is doing a run. We will have NI look into the situation, but we can not endorse this configuration for now.
We don't feel comfortable with less than 4 GB/s controllers for now.
$$$ Savings!! $$$: Most people should be buying the 8381 controller option. You'll need three parts for that: {PXI-8381 for the chassis, PCIe-8381 for the PC, MXI-Express cable to connect those}. You can save money by buying those as a bundle (3m cable length) by typing part number
782522-01into a search box at the NI web site.
We resisted recommending specific parts as long as possible, but people keep asking what to buy, so here it is, the basic NI parts list for those who will not be using a Whisper, and need "just a few" extra channels besides the imec data.
| Item | Part Number | $US |
|---|---|---|
| Chassis: | ||
| >>> PXIe-1071 chassis | 781368-01 | 1095.00 |
| >>> US power cord | 763000-01 | 0010.00 |
| Controller: | ||
| >>> PXIe-8381 module | 782362-01 | 1341.00 |
| >>> PCIe-8381 card | 782361-01 | 1341.00 |
| >>> MXI-Express cable 3m | 782317-03 | 0246.00 |
| >>>>>>> $$$ OR, 3-piece bundle $$$ | 782522-01 | 2571.00 |
| Multifunction IO: | ||
| >>> PXIe-6341 module | 781052-01 | 1176.00 |
| >>> BNC-2110 breakout box | 777643-01 | 0423.00 |
| >>> SHC68-68-EPM Shielded Cable 2m | 192061-02 | 0158.00 |
- Prices do not include service contracts.
- All required software is free.
fin