MWorks and National Instruments I/O module?

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Hi Chris -

Ahmad (CC’ed, a new postdoc in the lab) is considering to build a set up for recording with neuropixels instead of Blackrock. My understanding is that most neuropixels setups collect non-neural data (trial event codes, etc) on a National Instruments IO module - but I somehow remember that this is not compatible with MWorks. Is that correct?

As you know, we currently send all non-neural data from MWorks to Blackrock. So I could imagine that the easiest way forward might be to continue to do exactly that, while also sending some sync signal to the National Instruments I/O module? We would then have to also merge data from the two files (Blackrock + National Instruments).

Does all that sound right to you? Do you happen to know any labs (maybe Mehrdad’s?) who are using MWorks to run experiments with neuropixels?

Many thanks!
Yasmine

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Hi Yasmine,

My understanding is that most neuropixels setups collect non-neural data (trial event codes, etc) on a National Instruments IO module - but I somehow remember that this is not compatible with MWorks. Is that correct?

As far as I understand, at present, Neuropixels probes must be used with the Neuropixels PXIe card, which in turn needs to be installed in an NI PXI chassis. This poses two obstacles to using Neuropixels with MWorks:

  1. NI no longer supports their driver software for macOS, but even when they did, PXI support wasn’t included.
  2. The drivers needed to communicate with Neuropixels are only available for Windows.

There’s a bit more info in this discussion, but the upshot is that, currently, there’s no way for MWorks to communicate directly with a Neuropixels system.

It’ll be interesting to see what the requirements are for the (not yet available?) Neuropixels OneBox. That does not require a PXI chassis, but it’s possible that it will still rely on Windows-only drivers.

As you know, we currently send all non-neural data from MWorks to Blackrock. So I could imagine that the easiest way forward might be to continue to do exactly that, while also sending some sync signal to the National Instruments I/O module?

I’m not 100% clear on what comprises a complete Neuropixels setup. I think you need a Windows PC running NI software to control the PXI chassis and collect the data, although I’m not sure. But as long as the system includes some general-purpose digital input lines, I think what you suggest will work.

Do you happen to know any labs (maybe Mehrdad’s?) who are using MWorks to run experiments with neuropixels?

Sorry, I don’t.

FYI, I’m going to be on vacation for the next two weeks. If you need further assistance with this, I can help you when I return.

Cheers,
Chris

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Hi Chris -

Thanks for this info.

I’ll reach out to Mehrdad to see how his lab is overcoming these obstacles. And yes - would be good to connect about this when you return.

Happy vacation!
Yasmine

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Hi Yasmine,

Have you made any progress with answering your remaining questions regarding MWorks and Neuropixels? Another MWorks user asked a similar question about sending sync signals from MWorks to a Neuropixels system, so I was wondering if you had any new info I could share.

Thanks,
Chris

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Hi Chris -

I emailed with Gabe (postdoc in Mehrdad Jazayeri’s lab) and he confirmed that there is no way of having MWorks communicate directly with the neuropixels system. Perhaps you can touch base with him briefly before sharing the info he shared with me below?

Gabe explained that:

The imec card (which receives the neuropixels data) is on its own clock and it has only a single digital input (which can be accessed via the SMA port on the card). So, no matter what system you use, the neural data will be on a different clock than the non-neural data and will therefore need to be aligned via some common input.

And the current solution in the Jazayeri lab is as follows:

We simply have a sync signal (a ttl pulse generated by an arduino) that is shared in the two data streams and allows us to align the data streams posthoc. That should work for most use cases, unless you’d like to do a closed-loop experiment (e.g. trigger something in mWorks based on some feature in the neural activity).

Hope this helps!
Yasmine

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Hi Yasmine,

Thanks for sharing this info. I found a description of the SMA connector in the Neuropixels manual, which confirms what Gabe said.

The manual also linked to System Requirements for Neuropixels, which goes in to a lot of detail about specific hardware requirements for a Neuropixels system. In particular, this (from the section Acquisition: NI multifunction IO) may be of interest:

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.

This is specifically a feature of the SpikeGLX acquisition software, not Neuropixels in general. Also, they don’t say exactly how the data are “tightly synchronized”. Still, this might give you a way to send a rich stream of data (i.e. more than a single bit) from MWorks to a Neuropixels system, similar to what you currently do with Blackrock.

Cheers,
Chris

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Thanks Chris! Let me run this by Gabe and see what he thinks!

Yasmine