>> Updated: September 18, 2025 <<
Topics:
A PXIe chassis is basically an extension of the PCIe bus in your computer.
Before PXIe, you added expander cards directly into a workstation. A PXIe chassis adds extra slots and a convenient housing to hold plug-in PXIe "modules." This is a flexible and tidy way to interface computers to laboratory equipment.
IMPORTANT: Never insert/remove modules when a PXIe chassis is powered on.
PXIe is an industry standard covering:
You can mix and match components {controller, chassis, cards (modules), cables} from different manufacturers and they should mostly work together. There are some rules, though:
imec cards
The imec Neuropixels base-station modules will function with any PXIe components. So you can buy controllers and chassis from anybody.
Auxiliary I/O cards
SpikeGLX speaks to I/O modules using a National Instruments (NI) library called DAQmx, and this is unique to NI modules. You can only use NI I/O modules, but they can plug into non-NI chassis and controllers.
More than 5 imec cards
Generally, a PXIe backplane bus is organized into segments. Slots 1-6 are on segment 1, slots 7-12 are on segment 2, and 13-18 live on segment 3. These bus segments do not inherently talk to each other unless configured to do so in software. SpikeGLX does that using a chassis control package called NI-VISA, which is part of the NI Platform Services driver set. We do not know if this will work with very wide chassis from non-NI makers. So at present, if you need to run imec modules in more than five slots, we advise getting an NI chassis so the NI-VISA command set will definitely work.
Consult this guide to:
You can have at most one PXIe chassis, but that can have many card slots. Daisy chaining of chassis is not supported at this time.
A Thunderbolt-based controller can be used with a Thunderbolt-equipped laptop. That allows a very compact and portable setup. The limitation is that laptops are not suitable for running very large numbers of probes. That should be done on a workstation equipped with higher power CPU, larger power supply and better cooling system.
For a workstation computer you should avoid Thunderbolt controllers. In our experience, Thunderbolt has connection stability issues in general, but it is much worse on workstations where Thunderbolt seems to be an afterthought. We've discussed what to purchase based on probe count here.
You can run a mixture of OneBoxes and PXIe basestations in the same SpikeGLX run.
DAQmx talks to any NI card {PXIe, PCIe, USB}. That is, you are not limited to using an NI I/O card that plugs into a chassis.
The figure shows an NI 1071 chassis. It has 4 slots, all of them are populated here:
Thunderbolt controller module. Note that the chassis controller is special in that it MUST be in slot #1. It does not matter which slots you use for any the other modules. There are two Thunderbolt connection ports on this controller and it doesn't matter which one you use, the other will be unused. Note too that chassis come with slot blank-off plates. You should place these over any unused slots to optimize chassis cooling.
Imec module. A probe is plugged in at port 1, and another at port 3. It doesn't matter which ports you use and which are empty (except for quad-base), you just have to tell SpikeGLX where you actually plug in probes by checking those boxes in the Probe table. Also note that there is an SMA cable attached at 'TRIG' which runs to the NI breakout box sitting on top of the chassis. It is vital that each recording device gets wired with the common sync wave.
Imec module. Note especially that nothing is connected to the sync SMA connector. It is vital that ONLY ONE imec module SMA is connected. All the other imec modules will share the signal on the backplane. Connecting more than one SMA creates beat patterns which corrupt the signal. That rule applies whether the single SMA is configured for sync output or input. All other imec modules in the same chassis will automatically share that signal.
NI 6341 multifunction I/O module. This module is cabled to an NI BNC 2110 breakout box that provides convenient terminals to connect I/O signals. You can see that some unused BNC connectors have 50-ohm terminator caps applied. This suppresses crosstalk on unused channels. Unlike the imec modules, NI devices DO NOT get sync signals on the backplane. Rather, we added a cable from slot 2 to the NI breakout box to manually share the sync signal.
Sync in SpikeGLX works by sending a single common 1 Hz square wave to one channel of each recording data stream. The rising edges of this wave can then be matched across streams, and paired edge offsets can be used to map event times from one stream to another (our TPrime tool does this mapping). We discuss how this works in detail here.
Quick notes about imec PXIe modules:
SMA TRIG on the module front panel is the SYNC port. It uses 0-5V TTL (digital) signals.
Note: The OneBox 'SMA 1' and PXIe 'TRIG' are each in parallel with a 1 KOhm pull-up resistor. If that's too low an impedance for your signal source, then you can add a 100 Ohm pull-down resistor to your output line to compensate (add a BNC T with a 100 Ohm resistor on the unused branch between signal and shell).
In SpikeGLX, on the Configuration dialog Sync tab, you can select one device in the run for Sync output. This can be a separate pulser device, an NI device, a OneBox, or a PXIe module. All the other devices in that run must then be wired to receive that common shared Sync signal. If you select an imec module as output (generator) you don't have to run wires to the other imec modules in the chassis because the backplane already connects them. But you have to run wires to each OneBox and to any NI device.
Likewise, if you selected NI or a OneBox as the generator, you'd have to run a wire to the NI device if using that, and run a single wire to one (and only one) of the imec modules in the chassis. You specify which imec module is getting the input wire on the Sync tab.
Any imec module or OneBox in a run that is not selected for Sync output is automatically programmed for Sync input, so that it will record the common shared Sync signal being generated by the selected output device.
PXIe modules all live in the same PXIe chassis and share signals among themselves using the chassis backplane. So only one PXIe SMA should be connected whether bringing signals in or out of the chassis as a whole. However, if using more than one OneBox, there is no backplane connecting these, so you will need to cable up the SMA 1 connector of each OneBox in the run.
When Sync is disabled on the Sync tab, imec PXIe modules and OneBoxes are programmed for input at their Sync SMA. This allows you to record whatever 5V TTL signal you wish in the SY channels (bit #6) of each of the recorded data streams.
Main
Each port
Work through these sections in the order given.
Start with the hardware:
Notes:
For some chassis models, the chassis power is under control of the PC. When the PC starts up the chassis will automatically start up too.
Some chassis have manual power control. For these, start the chassis first, then the PC.
For Thunderbolt, start the PC and chassis separately, then when both are running, connect the cable. This may cause everything to freeze (Blue Screen of Death). Just try again if that happens.
Follow manufacturer recommendations for installing drivers your specific controller and chassis:
Notes:
If it seems like you don't need drivers at all, it's probably because Windows has installed a default driver for you. We nevertheless advise seeking the current recommendations from the vendor. Generally, the most recent version is a good choice.
For any installer, go with the default options.
However, if you get a choice, we advise that you DO NOT select automatic updates for your hardware. Once you have a working set of drivers it is best to keep using that version. It isn't necessary to have the latest version, and the updater may interrupt data acquisition runs at very inopportune times.
Keysight
You're looking for 'PXIe Chassis Family Drivers.'
ADLink
Click on the 'Drivers' link for your chassis model, but generally, you're looking for something called 'ADLink PXI Platform Services.'
National Instruments (NI)
Using NI I/O devices to add supplementary non-neural channels to your experiment is completely optional. SpikeGLX will work with multifunction I/O S-series 61XX, M-series 62XX, X-series 63XX devices, and with digital-only 653X devices. Moreover, you can use PXIe, PCIe or USB devices, though USB is slower and should be avoided for new purchases.
Regardless of the NI device model and format you will need NI DAQmx drivers to run it from SpikeGLX:
NI-MAX is a GUI application that lets you Inspect and test your NI hardware and software, like a fancy NI control panel. It will be installed automatically if you install either 'NI Platform Services' or 'DAQmx.'
It's not essential to have this, but it's kind of informative. When your NI hardware is configured properly, you will see your NI chassis listed on the left and you will see your NI controller and any NI cards shown "under" the chassis, meaning they are identified as being installed inside the chassis. That's reassuring.
This software only recognizes NI parts. Other brands of chassis and controller don't show up here, and importantly, imec cards do not show up here. That's normal.
The imec modules require driver software from 'enclustra.' Get that from our download site here and follow the included instructions.
Release downloads come with two executables:
Continue set-up using the SpikeGLX app that suits you.
From time-to-time imec updates the API software that GUI programs like SpikeGLX and Open Ephys use to talk to the hardware. Each version of the imec API is designed to work with certain versions of the firmware loaded in the PXIe module.
When you click 'Detect' SpikeGLX will test if the firmware has the correct version. If not, you will be instructed to use menu item Tools::Update Imec PXIe Firmware, to install the firmware included in your SpikeGLX download package. Follow the instructions in that dialog to perform this step.
The last part of setting up your PXIe-based system is to choose which PXIe slots you want to display in the big Probe table on the Devices tab of the Configuration dialog. That's the table showing all the places you can plug in your probes.
Devices tab, click Enable Imec.Configure Slots. In the dialog's table, there is a row for each PXIe slot, and each OneBox.Generally, NP 1.0-like headstages only have 1 dock per port, meaning you can only plug one probe into those headstages. So in the table we can keep things simpler by only showing one dock per port. That works great if you only use 1.0 parts.
However, 2.0 headstages generally can take two probes, so they have two docks. You have to be able to say whether you plugged into dock 1 or dock 2, so you need those options to be available in the Probe table. So you need 2 docks/port in this case.
Full details on the Configure Slots dialog are here.
Please read the User Manual, but at least read these sections:
The reading will explain in general how output files are named and their data formats. Here we follow that up with an illustrative example.
Simple Example
Suppose you want to run with your PXIe components:
If you named the run AAA, this would result in four data files:
Probe files:
AAA.g0_t0.Probes table imec0.ap files contain full-band data. Note that dual-band probes (such as NP 1.0) can generate both ap and lf files.AP channels, followed by one SY word containing error and sync data bits.Probe recording is the same whether you plug into OneBox or PXIe!
NIDQ files:
AAA.g0_t0.XA channels, followed by a single XD word containing the digital channel data.The governing sample clock for probes is in the headstage. All headstages run asynchronously, so you will need to align/sync data from different probes. The nominal sample rate for a headstage is ~30 KHz.
NI devices have programmable sample rates. You will configure your desired rate in the NI Setup tab of the Configure dialog.
As always, we recommend doing a calibration run for all the components you will enable in the same run. This greatly improves the estimates of their relative rates and will enable TPrime to accurately align the streams even for very long recording sessions. Find full discussion of synchronization and calibration here:
Note that clock rates vary with temperature so no single rate can accurately account for drift over long time spans. Rather, the common shared sync wave is used by the TPrime postprocessing tool to precisely determine current relative drift at any point in a run, provided the same sync wave edges can be paired. A good calibration ensures edges can be paired (based on the nominal rate estimate) even for long run durations. See help document: Sync: Aligning with Edges.
To run a probe with an imec PXIe module:
Enable Imec checkbox to enable the big Probes table.enable checkbox for that (slot,port,dock) in the Probes table.Detect.IM Setup tab to set addition parameters for the probe.Detailed instructions for the IM Setup tab are here.
To enable recording from an NI module:
Enable NI-DAQ checkbox to enable NI input features.Detect.NI Setup tab to set additional NI parameters.Detailed instructions for the NI Setup tab are here.
Don't forget to also:
- Set up your sync cabling
- Enable Sync on the
Synctab- Set your gate and trigger modes
- Name the run on the
Savetab
NI Output
Some NI I/O devices are capable of generating output signals. Generally, output features are managed by remote scripting and NOT in the Acquisition Configuration dialog:
Set digital outputs and/or DAC voltages during a run using the SDK remote interface functions. That's a separate add-on package you can learn about here.
Learn about using the WavePlayer features here.
You have a Thunderbolt controller link which has stopped talking. In that case:
If you can't connect to the imec modules it may be that the enclustra drivers need to be reinstalled. This happens often when Thunderbolt needs to be restarted:
If you don't have the 'Scan for New Hardware' menu item, then un/plug the Thunderbolt cable and try again.
fin